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At least 505 records · Page 28

SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles

Small-angle x-ray scattering (SAXS) is a powerful technique for assessing macromolecular structure. High-throughput SAXS is limited by the time-consuming and, at times, subjective nature of SAXS data interpretation. Here, we present SAXS Assistant, a Python-based script that streamlines SAXS data analysis to extract features for machine learning (ML) and key structural parameters, including the Guinier radius of gyration (R g ), pair distance distribution function (PDDF)-derived R g , maximum particle dimension (D max ), and Kratky plots. The script builds upon BioXTAS RAW and validates reliability via Guinier/PDDF R g agreement, an important indicator of well-measured data sets. For assistance in D max estimation, a multilayer perceptron regressor was trained with 1940 data files from the Small Angle Scattering Biological Data Bank. The model achieved a test set performance R 2 = 0.90 and mean absolute error = 11.7 Å. Training exclusively with experimental data translates analyses from researchers, including experts in the field, to the ML model, which helps assess D max estimations from PDDF. Gaussian mixture model clustering was implemented to classify profiles into structural classes based on entries in the Small Angle Scattering Biological Data Bank. Users may therefore assess the similarity between experimental samples and known biomolecular shapes within the mapped repository entries. This probabilistic clustering aids in quantifying information from Kratky and generating shape-descriptive features. SAXS Assistant accelerates SAXS data analysis through enforced quality control, ML-ready outputs, and flags for low-confidence results. In addition to providing the ability to analyze large data sets at high throughput, this tool is versatile and may serve researchers in both biological and synthetic polymer research fields.

36 MATERIALS SCIENCE↗

Influence of graphite geography on the yield of mechanically exfoliated few-layer graphene

Some of graphene's exciting properties that inspired countless studies over the last two decades are exclusive to defect-free, few-layer graphene (FLG, ≤4 layers) produced by mechanical exfoliation. Despite graphite exfoliation having been thoroughly studied, the influence of the graphite source on the successful exfoliation of FLG remains unexplored. Here, in this work, we examine the physicochemical properties and exfoliation performance of various graphite types (e.g., natural crystalline flake, natural vein, and synthetic) from around the globe (e.g., Alaska, Tanzania, China, etc.). We first established a normalization method for the facile comparison of FLG (Φ) yields between separately exfoliated graphites. Using this approach, we find that the relative yield of FLG ranges from 0% to 22% across graphite types, with regular natural crystalline flakes (NCF-R) performing the best overall (Φ NCF-R = 16% ± 5%). FLG yield was also found to depend on source geography, evidenced by Φ NCF-R ranging from 8% to 22% for NCF-R sourced from Alabama and Canada, respectively. We employed machine learning and Pearson correlation analysis to determine the graphite characteristics that govern FLG yield. Graphite source-dependent properties such as graphite surface area and mineral impurities, including aluminum and calcium, were found to be critically important. Our findings highlight the importance of the graphite source when trying to maximize the yield of mechanically exfoliated FLG and represent an important step toward producing higher quantities of defect-free FLG for graphene-based research.

42 ENGINEERING↗

Most of the rhamnogalacturonan-I from cultured Arabidopsis cell walls is covalently linked to arabinogalactan-protein

To characterize a purified rhamnogalacturonan-I (RG-I) containing both RG-I and arabinogalactan-protein (AGP) types of glycosyl residues, an AGP-specific β-1,3-galactanase that can cleave the AG backbone and release the AG sidechain was applied to this material. Carbohydrate analysis and NMR spectroscopy verified that the galactanase-released carbohydrate consists of RG-I covalently attached to the AG sidechain, proving a covalent linkage between RG-I and AGP. Size exclusion chromatography-multiangle light scattering-refractive index detection revealed that the galactanase-released RG-I has an average molecular weight of 41.6 kDa, which, together with the percentage of pectic sugars suggests an RG-I-AGP comprising one AGP covalently linked to two RG-I glycans. Carbohydrate analysis and NMR results of the RG-I-AGP, the galactanase-released glycans, and the RG lyase-released glycans demonstrated that the attached RG-I glycans are decorated with α-1,5-arabinan, β-1,4-galactan, xylose, and 4-O-Me-xylose sidechains. Furthermore, our measurement suggests that the covalently linked RG-I-AGP is the major component of the traditionally prepared RG-I.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanistic pathways and role of oxygen in oxidative coupling of methane derived from transient kinetic studies

Oxidative coupling of methane (OCM) is a promising industrial process to upgrade natural gas to high value chemicals. In this study, Temporal Analysis of Products (TAP) and steady-state experiments were conducted to distinguish how the composition of surface and gas phase oxygen influence mechanistic details of the selective conversion of CH 4 to C 2 H 4 over the Mn-Na 2 WO 4 /SiO 2 catalyst. The results from TAP studies indicate that methane activation on this catalyst proceeds predominantly via a short-lived, transient surface oxygen species and there is a competition for this species to form either CO or methyl radicals on the surface. This active species has a total lifetime of 3 s and is identified to have a dioxygen (e.g. O 2 2- or O 2 -) form. We show that the concentration of the transient surface oxygen species significantly impacts the OCM performance. Oxygen attributed to the catalyst lattice (in a singular form e.g., O - ), is found to activate methane to a lesser degree, but exclusively forms CO 2 . Evidence for these surface pathways for methyl radical, CO and CO 2 formation identified by TAP are also validated through steady-state experiments. Finally, by distinguishing different catalyst oxygen species and their role in selective/nonselective pathways, important screening criteria have been identified for the advancement of superior catalyst formulations.

36 MATERIALS SCIENCE↗

Na + -gated nanochannel membrane for highly selective ammonia (NH 3 ) separation in the Haber-Bosch process

Currently, cryogenic condensation is the predominant process for recovering ammonia (NH 3 ) in the Haber-Bosch (HB) process, which is highly energy intensive. To be more compatible with the reaction conditions in the HB process and thus minimize the pressure and temperature swing during reactant recycling, energy-efficient technologies for NH 3 extraction at elevated temperature and pressure are greatly needed. In this work, the Na + -gated nanochannel membrane, shown exclusively for water conduction in our previous work, also exhibited highly NH 3 -selective performance, with NH 3 /H 2 selectivity as high as 4,280 and NH 3 /N 2 selectivity > 10,000 at temperature up to 250 °C and pressure up to 35 bar. Excellent stability of the Na + -gated nanochannel membrane was demonstrated during a 100-h run in ternary NH 3 /H 2 /N 2 gas mixture at 200 °C and 35 bar, consistent with structural characterization by X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and Fourier transfer infrared (FTIR) spectroscopy. A techno-economic analysis (TEA) was conducted for the HB process using the Na + -gated nanochannel membrane and the traditional HB process with condenser. Finally, under the optimized separation conditions, > 80% energy savings and approximately 20% reduction of the net NH 3 production cost can be achieved, demonstrating the great potential of the Na + -gated nanochannel membrane for NH 3 separation in the HB process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NO formation by N 2 /O 2 plasma catalysis: The impact of surface reactions, gas-phase reactions, and mass transport

Pathways and timescales relevant to facilitate plasma-assisted N 2 -O 2 reactions are assessed by measuring the consumption of plasma-derived N and the formation of NO in the gas phase and over Ag catalytic surfaces. These measurements are enabled by a setup that enables N 2 activation in an atmospheric pressure RF plasma jet, enables O 2 addition in the plasma afterglow, facilitates reactions over an Ag wire catalyst, and allows species density quantification by molecular beam mass spectrometry. Gas-phase reactions consume N but do not form NO with high selectivity. The presence of the non-porous Ag wire catalyst increases the rate of N conversion to NO, though mass transfer processes, not surface reactions, dictate the rate of N consumption. When O 2 concentrations and the ratio of the surface area of the catalyst to the void volume of the reactor are high (3–5 mol% O 2 , 10900 m –1 ), N conversion to NO reaches 100 % selectivity. When both N 2 and O 2 are fed through the plasma jet, gas-phase NO production increases 10×, although plasma and gas-phase processes do not exclusively produce NO. Above a threshold NO density, N cannot diffuse to the catalyst surface faster than it is consumed in the gas phase by reactions with NO. Furthermore, the use of heterogeneous catalysts to enhance plasma-driven N x O y formation and control N x O y product selectivity is limited to cases where diffusive transport of N from the gas phase to the catalyst surface is faster than consumption of N from gas-phase reactions with NO.

Engineering↗

Mechanism of ion pairing–induced co-ion penetration into the stern layer

In classical electric double layer (EDL) theory, co-ions—ions carrying the same charge as the electrode—are assumed to be excluded from the Stern layer because of electrostatic repulsion. However, ion pairing with adsorbed counterions may enable co-ions to access the EDL, a phenomenon that remains underexplored. Key questions therefore remain unresolved, including how deeply co-ions penetrate, how ion-specific properties govern them, and how ion pairing within the EDL differs from bulk solution. Here, in this study, we employ molecular dynamics simulations combined with well-tempered metadynamics to quantify co-ion penetration and ion-pairing thermodynamics at positively charged Mg-Al layered double hydroxide interfaces (σ = +20.6 μC/cm 2 ) in aqueous chloride electrolytes across 0.005–3 M range. We reveal a concentration-driven crossover: at dilute conditions, counterion–co-ion contact ion pairing (CIP) is thermodynamically unfavorable or only weakly favorable (ΔG CIP = +0.12 kcal/mol for Li + to −0.42 kcal/mol for K + ), leading to co-ion exclusion. As concentration increases (≥0.5 M), enhanced screening reduces surface repulsion and stabilizes CIP thermodynamics (ΔG CIP = −0.89 kcal/mol for Li + to −1.05 kcal/mol for K + at 3 M), enabling monovalent co-ions to penetrate the Stern layer following the hydration hierarchy K + > Na + > Li + , while divalent co-ions (Mg 2+ , Ca 2+ ) remain in the diffuse layer, forming only solvent-separated pairs. Comparison with bulk solution shows interfacial ion pairing is suppressed at low concentrations but converges to bulk-like thermodynamics at high concentrations, indicating surface effects vanish under strong screening. These results establish a quantitative framework linking ion-pairing thermodynamics to co-ion penetration and providing strategies to design electrochemical interfaces.

Co-ion penetration↗

Crimean-Congo hemorrhagic fever survivors elicit protective non-neutralizing antibodies that target 11 overlapping regions on glycoprotein GP38

Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, exclusive to Nairoviridae , is a target of protective antibodies and is a key antigen in preclinical vaccine candidates. Here, we isolate 188 GP38-specific antibodies from human survivors of infection. Competition experiments show that these antibodies bind across 5 distinct antigenic sites, encompassing 11 overlapping regions. Additionally, we show structures of GP38 bound with 9 of these antibodies targeting different antigenic sites. Although these GP38-specific antibodies are non-neutralizing, several display protective efficacy equal to or better than murine antibody 13G8 in two highly stringent rodent models of infection. Together, these data expand our understanding regarding this important viral protein and may inform the development of broadly effective CCHFV antibody therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of a novel starch-based temperature rise inhibitor on cement hydration and microstructure development: The second peak study

Temperature rise inhibitor (TRI) modifies the exothermic process of cement hydration at early age and mitigates the buildup of cumulative heat, which sheds new light on solving the thermal cracking issue. After the main hydration peak, a broader “second peak” appears and brings the cumulative heat back to normal level within 7 days (for additions less than 0.15%). This study shows that the “second peak” can be attributed, almost exclusively, to C{sub 3}S hydration while triggered by C{sub 3}A hydration. In a pure C{sub 3}S system, the heat flow is depressed by TRI during the main hydration peak but never recovers after. In a monophase system composed of C{sub 3}S, C{sub 3}A and gypsum or a real cement paste, the ongoing precipitation of ettringite helps to pump out TRI polymer from the pore solution and eliminate the restriction on C-S-H nucleation. Afterwards, the precipitation of C-S-H accelerates again to form the “second peak”.

36 MATERIALS SCIENCE↗

Evidence of formation of an amorphous magnesium silicate (AMS) phase during alkali activation of (Na-Mg) aluminosilicate glasses

Highlights: • No hydrotalcite-group phase is formed as Al preferentially incorporates into zeolites. • Mg forms an amorphous Mg silicate (AMS) phase. • AMS is a more depolymerized phase when compared to Mg silicate hydrate (M-S-H). • High charge density of Mg effectively stabilizes depolymerized silicates in AMS phase. • Existence of AMS phase should be considered as possibility in Mg-rich AAMs. There is some ambiguity regarding the fate of Mg during the alkali activation of Mg-rich precursors within the broader field of alkali activated materials (AAMs). The present work addresses this issue by studying the reaction products in AAMs synthesized from (Na-Mg) aluminosilicate glasses. Here, instead of magnesium silicate hydrate (M-S-H) phase, Mg exclusively forms an amorphous magnesium silicate (AMS) phase. Compared to M-S-H, AMS is a more depolymerized phase, which has not previously been well documented. The formation of AMS seems to be driven by the high charge density of the Mg cation which effectively stabilizes the depolymerized silicate species. We also show that the lack of hydrotalcite-group phases is due to aluminum depletion by zeolite formation. This work highlights the need to consider the existence of the AMS phase in Mg-containing AAMs, especially in complex systems, where its identification may be difficult.

36 MATERIALS SCIENCE↗

Specific molecular design of polycarboxylate polymers exhibiting optimal compatibility with clay contaminants in concrete

Highlights: • Allyl ether-based PCEs with short side chain length and low side chain density presented superior clay resistance. • PCEs with medium side chain density exhibited best clay robustness when compared at the absolute dosed quantities. • The proportion of PCE being intercalated into the layered structure of clay was quantified. It is widely recognized that the dispersing ability of polycarboxylate superplasticizers (PCEs) could be hindered due to the presence of clay contaminants in concrete. In this study, a series of allyl ether-based polycarboxylate superplasticizers possessing short polyethylene glycol side chains was successfully synthesized and probed for their clay tolerance. The resulting PCE polymers were characterized via Size Exclusion Chromatography (SEC) to obtain their molecular properties. Thereafter, their dispersing ability was probed in the absence and presence of sodium bentonite. Allyl ether-based polycarboxylate (APEG) polymers possessing short side chains were found to exhibit enhanced clay resistance as compared to that of conventional MPEG PCEs holding long pendant chains. The mode of interaction between APEG PCEs and bentonite was investigated via sorption and XRD measurements. The data revealed that APEG PCEs possessing a lower side chain density intercalate less into the interlayer space of bentonite than those exhibiting higher side chain density.

36 MATERIALS SCIENCE↗

Bulk Grain-Boundary Materials from Nanocrystals

Grain-boundary engineering is pivotal to fully utilize the mechanical, electrical, and thermal-transport properties of various materials. However, current methods in metallurgy rely almost exclusively on top-down approaches, making precise grain-boundary engineering, especially at nanoscale, difficult to achieve. Herein, we report a method to produce tailored grain-boundary conditions with nanoscale precision from colloidal metal nanocrystals through surface treatment followed by a pressure-sintering process. The resulting bulk grain-boundary materials (which we call “nanocrystal coins”) possess a metal-like appearance and conductivity while inheriting the original domain features of the nanocrystal building blocks. In this work, nanoindentation measurements confirmed the superior mechanical hardness of the obtained materials. Further, we use this method to fabricate, for the first time, a single-component bulk metallic glass from amorphous palladium nanoparticles. Our discovery may spur the development of new materials whose functionality crucially depends on the domain configuration at nanoscale, such as superhard materials, thermoelectric generators, and functional electrodes.

36 MATERIALS SCIENCE↗

A machine-learning framework for the simulation of nuclear deflection of Planet-Killer-Asteroids

Here, as detection capabilities in astronomy have dramatically improved over the last two decades, concerns over Planet-Killer-Asteroids (PKAs) have become widespread, with nuclear weapons being proposed to destroy or deflect asteroids that are on a short-term projected collision course with Earth. Two main mitigation strategies have been proposed: • Case 1: Break up an incoming asteroid into smaller pieces that will disperse widely, resulting in smaller-scale, less detrimental, Earth-impacts or • Case 2: Deflect an incoming asteroid trajectory to avoid collision altogether. While the two strategies are not mutually exclusive, deflection is a safer strategy, ideally by harnessing all of the released energy from a nuclear device to move the asteroid as a rigid body. However, this case may not be always possible, since the strength of the energy release may break up the asteroid. In this work, the dynamical response of a PKA to a series of ultra-high energy impulses, such as those generated by nuclear devices, is formulated. A rapid iterative Discrete Element Method (DEM) method is developed to describe the deflection and potential breakup of the PKA as a function of a material bonding strength parameter within the asteroid and the magnitude of the applied impulse. The use of DEM allows for fragmentation of the PKA and the ability to compute the trajectories and distribution of the resulting debris field. Finally, a machine-learning algorithm is then developed and combined with the DEM approach to optimize the pulsation strategy for maximum possible safety and success.

42 ENGINEERING↗

Effect of CO 2 on the water slip flow at silica surfaces for nanometer slit pores of talc

In our previous study, Molecular Dynamics (MD) simulated water flow with no dissolved gas in nanometer slit pores of the hydrophobic talc surfaces revealed a slip length of about 0.5 nm, which is close to the size of “water exclusion zone” but much less than experimental slip length. Atomic Force Microscopy (AFM) imaging confirmed the presence of pancake shape nanobubbles at the hydrophobic talc (001) surface (size from tens to hundreds of nanometers). The effect of CO 2 on water slip flow in talc nanopores is reported to reveal the importance of dissolved gas for confined fluid flow. MD simulated 7 nm CO 2 nanobubbles were found to attach and spread at the talc (001) surface, consistent with the AFM observation. Simulated CO 2 saturated water flow in the slit pores of talc (001) surfaces predicted the generation of CO 2 nanobubbles at the end of the slit pore, due to the stabilization of a CO 2 film at the talc (001) surfaces and a water barrier at the edge surfaces of talc. A “critical thickness” of about 1.5 nm was found for CO 2 nanobubbles to be stabilized at the end of the talc (001) surface. With 1.5 nm CO 2 nanobubbles at the talc (001) surface of a 6 nm slit pore, a water slip length of 1.8 nm was determined. Furthermore, the nanometer slit pore simulations with dissolved CO 2 in water revealed an increased slip length. It is expected that an increased slip length value would be found with an increased CO 2 film thickness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A comprehensive experimental and kinetic modeling study of di-isobutylene isomers: Part 1

We report di-isobutylene has received significant attention as a promising fuel blendstock, as it can be synthesized via biological routes and is a short-listed molecule from the Co-Optima initiative. Di-isobutylene is also popularly used as an alkene representative in multi-component surrogate models for engine studies of gasoline fuels. However, there is limited experimental data available in the literature for neat di-isobutylene under engine-like conditions. Hence, most existing di-isobutylene models have not been extensively validated, particularly at lower temperatures (< 1000 K). Most gasoline surrogate models include the di-isobutylene sub-mechanism published by Metcalfe et al. with little or no modification. The current study is undertaken to develop a detailed kinetic model for di-isobutylene and validate the model using a wide range of relevant experimental data. Part 1 of this study exclusively focuses on the low- to intermediate temperature kinetics of di-isobutylene. An upcoming part 2 discusses the high-temperature model development and validation of the relevant experimental targets. Ignition delay time measurements for the di-isobutylene isomers were performed at pressures ranging from 15 - 30 bar at equivalence ratios of 0.5, 1.0, and 2.0 diluted in air and in the temperature range 650 - 900 K using two independent rapid compression machine facilities. In addition, measurements of species identified during the oxidation of these isomers were performed in a jet-stirred reactor and in a rapid compression machine. A detailed kinetic model for the di-isobutylene isomers is developed to capture the wide range of new experimental targets. For the first time, a comprehensive low-temperature chemistry submodel is included. The differences in the important reaction pathways for the accurate prediction of the oxidation of the two DIB isomers are compared using reaction path analysis. In conclusion, the most sensitive reactions controlling the ignition delay times of the DIB isomers under the pressure and temperature conditions necessary for autoignition in engines are identified.

09 BIOMASS FUELS↗

O 2 -Dependence of reactions of 1,2-dimethoxyethanyl and 1,2-dimethoxyethanylperoxy isomers

Reaction mechanisms of Ṙ and ROȮ radicals derived from low-temperature oxidation of 1,2-dimethoxyethane (CH 3 O(CH 2 ) 2 OCH 3 ) were investigated using speciation from multiplexed photoionization mass spectrometry (MPIMS) measurements via Cl-initiated oxidation, in conjunction with electronic structure calculations. The experiments were conducted at 5 bar, from 450 K – 650 K, and O 2 concentrations from 1 · 10 14 cm –3 – 6 · 10 18 cm –3 to probe the effects on competing reaction channels of 1,2-dimethoxyethanyl (Ṙ) and 1,2-dimethoxyethanylperoxy (ROȮ) isomers. Several species were detected with photoionization spectral fitting – ethene, formaldehyde, methyl vinyl ether, and 2-methoxyacetaldehyde – and, as determined by electronic structure calculations, may form via unimolecular decomposition of 1,2-dimethoxyethanyl or 1,2-dimethoxyethanylperoxy. O 2 -dependent yield ratios show that the formation pathways for all species undergo a competition between O 2 -addition and unimolecular decomposition. Here, adiabatic ionization energies were also calculated and utilized along with exact mass determinations to infer contributions for other species derived exclusively from first- and second-O 2 -addition, including 1,2-dimethoxyethene, cyclic ethers, and dicarbonyls.

1,2-dimethoxyethane↗

A finite difference informed random walker (FDiRW) solver for strongly inhomogeneous diffusion problems

In nature, many complex multi-physics coupling problems exhibit strong diffusivity inhomogeneity. For instance, in the context of radionuclide absorption by porous wasteform materials within a flowing waste stream, the difference of species’ diffusivity in solid and liquid phases spans by 3~8 orders of magnitude. To solve the diffusion equations with strongly inhomogeneous diffusivity, traditional discretization-based methods, such as the Finite Difference Method (FDM), require infinitesimally small time steps (<10 -10 ) as high spatial resolutions are employed in most microstructure evolution processes, leading to prohibitively high computational costs. Here, this work developed an integrated numerical approach (FDiRW: Finite Difference informed Random Walk) to tackle this challenge. The idea is that utilizing the Random Walk concept, the fast diffusion is modeled as a superposition of point source’s solution for a concentration distribution while FDM is used to obtain the point source’s solution at each node. A mesh-coarsening algorithm is developed to generate an exclusive coarse mesh for FDiRW approach to maximize its efficiency. The effectiveness of the coarse mesh-based FDiRW approach is validated by benchmarking Finite Difference solutions. Numerical results demonstrated that FDiRW achieves a remarkable 1000x computational efficiency improvement over FDM while preserving desired accuracy for a medium-sized model of 192 × 192 × 192 grids. Finally, as models scale up, a floating-point operations (PLOPs) analysis of the FDiRW algorithm reveals that its computational complexity grows quadratically in terms of the number of nodes employed in computation.

36 MATERIALS SCIENCE↗