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Abstract The assessment and regulation of chemical toxicity to protect human health and the environment are done one chemical at a time and seldom at environmentally relevant concentrations. However, chemicals are found in the environment as mixtures, and their toxicity is largely unknown. Understanding the hazard posed by chemicals within the mixture is critical to enforce protective measures. Here, we demonstrate the application of bioactivity profiling of environmental water samples using the sentinel and ecotoxicology model species Daphnia to reveal the biomolecular response induced by exposure to real-world mixtures. We exposed a Daphnia strain to 30 sampled waters of the Chaobai River and measured the gene expression response profiles. Using a multiblock correlation analysis, we establish correlations between chemical mixtures identified in 30 water samples with gene expression patterns induced by these chemical mixtures. We identified 80 metabolic pathways putatively activated by mixtures of inorganic ions, heavy metals, polycyclic aromatic hydrocarbons, industrial chemicals, and a set of biocides, pesticides, and pharmacologically active substances. Our data-driven approach discovered both known bioactivity signatures with previously described modes of action and new pathways linked to undiscovered potential hazards. This study demonstrates the feasibility of reducing the complexity of real-world mixture toxicity to characterize the biomolecular effects of a defined number of chemical components based on gene expression monitoring of the sentinel species Daphnia.
X-ray photoelectron spectroscopy (XPS) is one of the most widely used techniques for surface characterization. Analysis of XPS data is challenging and requires the analyst to fit the data with synthetic line shapes to reach physically meaningful interpretations. Experimental spectral envelopes, however, are complex and display asymmetric features that are often ignored or attributed to additional chemical components. The high-resolution XPS spectra of [C 4 C 1 Pyrr][NTf 2 ] and [C 8 C 1 Im][NTf 2 ] all exhibit a degree of asymmetry which is systematically observed at the higher binding energy side of photoemission envelopes. Here, we present the development of a refined fitting procedure for XPS spectra of these ionic liquid-based systems which include (a) Shirley background offset necessary to account for the insulator-like region and (b) spectral asymmetry in C 1s and N 1s regions. Further, Shirley and trapezoid components are applied to compensate for inelastic scattering taking place during electron transitions as high as 7.8 eV above the start of the fitting region in C 1s high-resolution spectrum. To demonstrate the fitness of this model, we present an analysis of a 2:1 mixture of [C 4 C 1 Pyrr][NTf 2 ]: [C 8 C 1 Im][NTf 2 ].
Carbonyl sulfide (OCS) was used as a reaction gas to investigate gas phase metal (M + ) ion-molecule reactions using the Agilent 8900 inductively coupled plasma tandem mass spectrometer (ICP-MS/MS) to yield insight on how this gas may be used to remove isobaric interferences in analytical measurements. The experimental work was paired with density functional theory (DFT) calculations of the reaction enthalpy to predict whether M + will react with OCS. A multi-element standard containing 46 elements ranging from 9 to 208 u was analyzed in the presence and absence of OCS. When a reaction was observed, the dominant product was the sulfide (MS + ). Oxide products were also observed for many M + but formation was less efficient with OCS than previously observed with other reaction gases. This is likely due to the weaker OC-S bond that makes MS + formation more favorable. Increasing the flow rate from 0.1 to 0.2 mL/min (corresponding to a change in reaction gas pressure from 0.35 to 0.53 Pa (2.6 to 4.0 mTorr)) generally resulted in greater MS + production, including the secondary product MS 2 + for a few cations. The early lanthanide series ions (La + , Ce + , Pr + and Nd + ) produced greater quantities of MO + at the higher pressure, although MS + products were still the dominant product. The DFT-predicted reaction enthalpies were consistent with the observed sulfide formation, with an accuracy >90%; however, model predictions were less accurate for the minor and higher order products (< 77% for MO + ). Finally, the work presented here continues a systematic study of ion-molecule reactions in ICP-MS/MS to understand and develop new and novel ways to analyze complex mixtures with minimal pre-analysis treatment.
Using electron beam manipulation, we enable deterministic motion of individual Si atoms in graphene along predefined trajectories. Structural evolution during the dopant motion was explored, providing information on changes of the Si atom neighborhood during atomic motion and providing statistical information of possible defect configurations. The combination of a Gaussian mixture model and principal component analysis applied to the deep learning-processed experimental data allowed disentangling of the atomic distortions for two different graphene sublattices. This approach demonstrates the potential of e-beam manipulation to create defect libraries of multiple realizations of the same defect and explore the potential of symmetry breaking physics. The rapid image analytics enabled via a deep learning network further empowers instrumentation for e-beam controlled atom-by-atom fabrication. Here, the analysis described in the paper can be reproduced via an interactive Jupyter notebook at https://git.io/JJ3Bx.
We investigate the use of data-driven likelihoods to bypass a key assumption made in many scientific analyses, which is that the true likelihood of the data is Gaussian. In particular, we suggest using the optimization targets of flow-based generative models, a class of models that can capture complex distributions by transforming a simple base distribution through layers of nonlinearities. We call these flow-based likelihoods (FBL). We analyze the accuracy and precision of the reconstructed likelihoods on mock Gaussian data, and show that simply gauging the quality of samples drawn from the trained model is not a sufficient indicator that the true likelihood has been learned. We nevertheless demonstrate that the likelihood can be reconstructed to a precision equal to that of sampling error due to a finite sample size. We then apply FBLs to mock weak lensing convergence power spectra, a cosmological observable that is significantly non-Gaussian (NG). We find that the FBL captures the NG signatures in the data extremely well, while other commonly used data-driven likelihoods, such as Gaussian mixture models and independent component analysis, fail to do so. This suggests that works that have found small posterior shifts in NG data with data-driven likelihoods such as these could be underestimating the impact of non-Gaussianity in parameter constraints. By introducing a suite of tests that can capture different levels of NG in the data, we show that the success or failure of traditional data-driven likelihoods can be tied back to the structure of the NG in the data. Here, unlike other methods, the flexibility of the FBL makes it successful at tackling different types of NG simultaneously. Because of this, and consequently their likely applicability across datasets and domains, we encourage their use for inference when sufficient mock data are available for training.
Rotating detonation engines (RDEs) hold great promise as a technology for powering aviation engines. The pressure gain that results from continuously traversing detonation waves enables high theoretical performance compared to deflagration-based combustion. However, the harsh operating conditions inside an RDE restrict the availability of suitable experimental diagnostics to study these systems in detail and the range of spatial and temporal scales render numerical simulations of these systems difficult. In this study, we have combined adaptive mesh refinement and a robust shock-capturing approach to study RDE systems computationally using the compressible, reactive solver PeleC. Multi-species transport along with compressible Navier-Stokes equations are solved in the model along with finite-rate chemistry. Complex geometries are represented using an embedded boundary method with second-order spatial accuracy and the system is evolved in time using a second-order Runge-Kutta method. We present studies of a methane-air RDE system that is doped with varying levels of hydrogen. Our analysis focusses on how fuel mixture and doping levels effect the detonation flame structure and the generation of multiple wave modes.
Large-Eddy Simulations (LES) of a gasoline spray, where the mixture was ignited rapidly during or after injection, were performed in comparison to a previous experimental study with quantitative flame motion and soot formation data [SAE 2020-01-0291] and an accompanying Reynolds-Averaged Navier–Stokes (RANS) simulation at the same conditions. The present study reveals major shortcomings in common RANS combustion modeling practices that are significantly improved using LES at the conditions of the study, specifically for the phenomenon of rapid ignition in the highly turbulent, stratified mixture. At different ignition timings, benchmarks for the study include spray mixing and evaporation, flame propagation after ignition, and soot formation in rich mixtures. A comparison of the simulations and the experiments showed that the LES with Dynamic Structure turbulence were able to capture correctly the liquid penetration length, and to some extent, spray collapse demonstrated in the experiments. For early and intermediate ignition timings, the LES showed excellent agreement to the measurements in terms of flame structure, extent of flame penetration, and heat-release rate. However, RANS simulations (employing the common G-equation or well-stirred reactor) showed much too rapid flame spread and heat release, with connections to the predicted turbulent kinetic energy. With confidence in the LES for predicted mixture and flame motion, the predicted soot formation/oxidation was also compared to the experiments. The soot location was well captured in the LES, but the soot mass was largely underestimated using the empirical Hiroyasu model. An analysis of the predicted fuel–air mixture was used to explain different flame propagation speeds and soot production tendencies when varying ignition timing.
A rapid compression machine (RCM) has been applied to measure the ignition delay times of NH 3 /CH 3 OH mixtures covering pressures of 20 and 40 bar, equivalence ratios of 0.5, 1.0 and 2.0, and temperatures between 845 and 1100 K. Here the measurements show that the NH 3 /CH 3 OH mixtures become more reactive with increasing methanol addition. Addition of merely 1% (molar basis) of CH 3 OH to NH 3 lowers the ignition temperature around 100 K at 40 bar in comparison to pure NH 3 . The ignition delay is a complex function of fuel mixture and stoichiometry. For the 1% CH 3 OH mixture, the leaner mixtures are more reactive, while the reverse trend is found for mixtures with 5%, 20% and pure CH 3 OH. Analysis of the pressure profiles shows three distinct ignition modes for NH 3/ CH 3 OH mixtures, facilitated by the pre-ignition heat release from NH 3 consumption. A detailed mechanism for ignition of NH 3 /CH 3 OH fuel blends has been developed, capable of reproducing the ignition behavior of mixtures with reasonable accuracy. A subset for amine / methanol interactions was established, with rate constants for the key reaction between NH 2 and CH 3 OH calculated from ab initio theory. A sensitivity analysis indicates that the critical reactions during the auto-ignition process vary with the CH 3 OH mole fraction in the fuel. The ammonia chemistry, namely NH 2 + NO, NH2 + NO 2 and NH 2 + HO 2 , is dominant for the mixture with 1% CH 3 OH, while the reactions related to CH 3 OH and H 2 O 2 are more important for the 20% CH 3 OH mixture. The interaction between ammonia and methanol shows a more prominent effect on auto-ignition for mixtures with 5% CH 3 OH in fuel as compared to those with 1% and 20% CH 3 OH. According to the modeling results, methanol addition is found to enrich the O/H radical pool, consuming ammonia and promoting auto-ignition through different reaction pathways.
In this work, we present NENCI-2021, a benchmark database of ~8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation–π and anion–π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion–π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (E int ) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The E int values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) E int value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent—these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)- based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation–π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the E int values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive E int values, and maximum errors of ±0.2–0.3 kcal/mol (i.e., ~±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.
The aim of this program was to gain a fundamental understanding of the behavior of various guest molecules in nano-confined environments, such as metal organic frameworks (MOFs), using a combination of novel synthesis, ab initio modeling, and in situ characterization. Through this project, we developed a concise understanding of the mechanisms that control adsorption/desorption of gaseous molecules and their mixtures, leading to design/synthesis guidelines for MOFs with desired functionality. We further developed methods to disentangle kinetic from thermodynamic effects during adsorption, as well as to characterize the interactions at play. In the first funding cycle, the focus was on the unambiguously characterization of co-adsorption and diffusion of gasses/vapors and their mixtures. In the second funding cycle, the focus was on characterizing the effects of the nano-confinement on the kinetics and thermodynamics of adsorption processes inside MOFs, again with an emphasis on mixtures of gasses and vapors. The nano-confinement can tip the thermodynamic vs. kinetic balance, and current understanding and theory based on single-component analysis can lead to incorrect predictions for mixtures. This is of particular interest in real-world applications, where gasses/vapors are typically mixed, contain impurities, or are often exposed to humid conditions. Our main findings were: (i) within confined environments the adsorption behavior of mixed gasses/vapors can be drastically different from the “sum” of the corresponding single phases; (ii) co-adsorption is often competitive and detrimental to performance, but it can also be cooperative and beneficial; (iii) in some co-adsorbed gasses/vapors, molecules that are strongly bound in the single-component phase can be replaced by molecules that are nominally weaker bound (molecular exchange) due to guest-guest interactions that lower the kinetic barriers and favor the final adsorption state; (iv) kinetic and thermodynamic effects can be precisely controlled through pore-size engineering and synthesis; and, (v) kinetic effects can be identified and disentangled from thermodynamic effects during adsorption through a series of sequential and simultaneous gas loading measurements. The short-term goal of this program was the controlling and understanding of common MOF systems in real-world situations where gasses/vapors are mixed, which will have an important impact on industrial processes and applications from gas storage and sequestration to catalysis and sensors. The long-term goals include the development of theoretical and experimental methods for gaining a fundamental understanding of adsorption/reaction processes within MOFs, as well as new guidelines for synthesizing MOFs with tailored physical and chemical properties.
Poly(ethylene oxide) (PEO)-based electrolytes have gained increasing attention in both the rechargeable battery industry and fundamental research, but any influence of the ions on the polymer conformation is not fully understood. Small-angle neutron scattering (SANS) is a powerful means to determine single-polymer chain conformations. We conducted SANS experiments on 50:50 blends of perdeuterated PEO (dPEO) and hydrogenous PEO (hPEO) of two different molecular weights (20 and 40 kDa) doped with two different salts (LiTFSI and LiClO 4 ) at various concentrations. An additional measurement with LiI is also reported. The scattering profiles of salt-doped dPEO/hPEO blends were measured, and the incoherent scattering from dPEO and hPEO doped with salt was measured separately. A strong low q upturn was observed in some of the blends and in the pure dPEO homopolymers. The statistical segment lengths of PEO–salt mixtures were derived using a Kratky analysis. The segment length decreases modestly with increasing amounts of LiTFSI but apparently first increases then decreases with added LiClO 4 . At the highest salt concentration examined (r = [Li+]/[EO] = 0.125), a roughly 10% decrease in the statistical segment length was observed in both LiTFSI and LiClO 4 -doped PEOs, for both molecular weights. This work confirms that added salt causes a contraction of the PEO chain dimensions, but the effect appears slightly weaker than reported recently. Certain difficulties in data analysis are also discussed, including the unexplained low q scattering even in pure deuterated polymers, uncertainties in background subtraction, and inappropriate application of the Debye function.
The dissolution of polyethylene terephthalate (PET) is a critical step for a solvent-based process, yet it typically requires highly corrosive or toxic solvents. Here, we investigate the solubilization and conformational behavior of PET in binary mixtures of hexafluoro-2-propanol (HFIP) and dichloromethane (DCM) as a strategy to reduce HFIP usage while maintaining effective dissolution. Small-angle neutron scattering (SANS) measurements reveal that PET remains molecularly dissolved in HFIP/DCM mixtures up to 50 vol% DCM. Analysis of PET chain conformations shows a transition from Gaussian behavior at low HFIP fractions to more swollen chains at intermediate compositions, accompanied by a counter-intuitive minimum in the radius of gyration at 50% HFIP. Complementary SANS measurements of the binary solvents demonstrate that compositional heterogeneity is maximized at this same solvent composition, suggesting a direct coupling between solvent microstructure and polymer dimensions. Molecular dynamics simulations corroborate the experimental findings, revealing solvent domain formation, preferential solvation of PET by HFIP, and a “caging” effect arising from solvent heterogeneity that leads to polymer coil compaction. Together, these results provide molecular-level insight into polymer behavior in mixed solvent systems and establish HFIP/DCM mixtures as a promising, more sustainable solvent platform for the PET post-process.
Ammonia has garnered interest as an alternative fuel for power sectors with heavy payload and distance requirements, such as shipping. In this study, ammonia was used in a dual-fuel compression-ignition combustion strategy to overcome some of its technical barriers, using a diesel pilot to ignite a premixed mixture of ammonia and air. Mixtures of premixed ammonia and hydrogen were also explored to evaluate whether the inclusion of hydrogen improves nitrogen-based emissions from the combustion process. A single-cylinder version of a Cummins ISB 6.7 L engine platform was used to experimentally study these effects at various global air/fuel ratios and hydrogen energy fractions. Hydrogen inclusion produced pronounced NOx and N2O emissions, while inclusion of trapped residuals increased N2O but reduced NOx. The two most recent and relevant mechanisms available in the literature—those from Xu and Zhang-Ren-Kokjohn—were used in a chemical kinetics analysis to examine the observed differences in the NOx trends from two dual-fuel ammonia/diesel datasets: (1) in which a portion of the premixed ammonia was substituted with hydrogen and (2) in which the effect of hot trapped residuals was evaluated with only ammonia/air premixed mixtures. The analysis with both mechanisms showed agreement with experimental trends; however, contributions from thermal vs. fuel-borne NOx pathways showed disagreement. A reaction pathway analysis showed that the HNO to NO pathway was the key to NO formation in the mixture.
Using hybrid functional-based density functional theory calculations, we analyze the structure and kinetics of defects formed in two competing synthesis routes to prepare hydrogen-doped In 2 O 3 films, using a hydrogen and oxygen gas mixture vs synthesis in the presence of water vapor. For both of these synthesis routes, we find that H + is the dominant defect species: when the Fermi level is close to the conduction band, H + has a lower formation energy than other intrinsic or extrinsic defects. Our results also suggest that water molecules spontaneously split into H + (which occupies octahedral voids) and OH – interstitials (which occupies vacant oxygen lattice sites or oxygen vacancies). From the analysis of the binding energies between these different defects, we conclude that these defects do not cluster and are most likely to stay spatially distributed throughout the films. In addition, the sum of formation energies of an oxygen (i.e., O$^{2–}_i$) and a H + interstitial is close to the formation energy of a OH – interstitial, meaning that water molecules are completely split into 2H + and O$^{2–}_i$ at the synthesis conditions. Further, in the presence of H 2 + O 2 gas mixture, oxygen interstitials occupy oxygen vacancies while hydrogen interstitials occupy vacant oxygen lattice sites and form bonds with lattice oxygens. Our analysis of the defect equilibria suggests that the hydrogen content in films synthesized in the presence of water vapor is higher than films synthesized in the presence of a hydrogen gas mixture. At high dopant concentrations, a hydrogen bond network is formed in the system and this leads to large distortions in the lattice.
In this study, a method for characterizing the topological fluctuations in liquids is proposed. This approach exploits the concept of the weighted gyration tensor of a collection of particles and permits the definition of a local configurational unit (LCU). The first principal axis of the gyration tensor serves as the director of the LCU, which can be tracked and analyzed by molecular dynamics simulations. Analysis of moderately supercooled Kob–Andersen mixtures suggests that orientational relaxation of the LCU closely follows viscoelastic relaxation and exhibits a two-stage behavior. The slow relaxing component of the LCU corresponds to the structural, Maxwellian mechanical relaxation. Additionally, it is found that the mean curvature of the LCUs is approximately zero at the Maxwell relaxation time with the Gaussian curvature being negative. This observation implies that structural relaxation occurs when the configurationally stable and destabilized regions interpenetrate each other in a bicontinuous manner. Finally, the mean and Gaussian curvatures of the LCUs can serve as reduced variables for the shear stress correlation, providing a compelling proof of the close connection between viscoelastic relaxation and topological fluctuations in glass-forming liquids.
The molecular distribution at the liquid-vapor interface and evolution of the hydrogen bond interactions in mixtures of glycerol and choline chloride are investigated using X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. Nanoscale depth profiles of supersaturated deep eutectic solvent (DES) mixtures up to ~2 nm measured by ambient-pressure XPS show the enhancement of choline cation (Ch + ) concentration by a factor of 2 at the liquid-vapor interface compared to the bulk. In addition, Raman spectral analysis of a wide range of DES mixtures reveals the conversion of gauche-conformer Ch + into the anti-conformer in relatively lower ChCl concentrations. Finally, the depletion of Ch + from the interface (probing depth = 0.4 nm) is demonstrated by aerosol-based velocity map imaging XPS measurements of glyceline and water mixtures. The nanostructure of liquid-vapor interfaces and structural rearrangement by hydration can provide critical insight into the molecular origin of the deep eutectic behavior and gas-capturing application of DESs.
We develop an unsupervised probabilistic model for heterogeneous Electronic Health Record (EHR) data. Utilizing a mixture model formulation, our approach directly models sequences of arbitrary length, such as medications and laboratory results. This allows for subgrouping and incorporation of the dynamics underlying heterogeneous data types. The model consists of a layered set of latent variables that encode underlying structure in the data. These variables represent subject subgroups at the top layer, and unobserved states for sequences in the second layer. We train this model on episodic data from subjects receiving medical care in the Kaiser Permanente Northern California integrated healthcare delivery system. The resulting properties of the trained model generate novel insight from these complex and multifaceted data. In addition, we show how the model can be used to analyze sequences that contribute to assessment of mortality likelihood.