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Differential energy losses of fission fragments in thin carbon films as function of mass and initial energy mapped by time of flight method
Photothermodissociation (PTD) of an isolated molecule is the name of the process when a photon is absorbed by an electronic transition, the energy is transferred to the vibrations (hot molecule) and then an atom or a fragment is ejected. A statistical physics treatment is presented that goes beyond the thermal approximation and fully takes into account the isolation of the system. A model is given that permits an explicit calculation of the ejection rates of hydrogen and carbon fragments from aromatic molecules as a function of their size and internal energy. Then, the lifetime of species against PTD in different astronomical radiation fields will result when a precise dynamical evolution of their internal energy can be established.
A better understanding of the chemical properties of organic aerosol (OA) particles will improve our ability to characterize their sources and predict their lifetime. The high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is widely used to measure OA in real time using thermal vaporization followed by electron ionization (EI). EI creates fragment ions that can be assigned to functional groups using delta analysis, a method of classifying mass spectra according to the presence of different chemically related ion series. In this study, we demonstrate the application of delta analysis to characterize molecular structures using a new visualization method. We also use delta analysis to quantify the functional group distribution with an average absolute error of ∼5–6% for individual standard molecules, comparable to the error observed for OA mixtures from biomass and coal combustion fit with Fourier transform infrared spectroscopy. Finally, we apply delta functional group analysis to AMS positive matrix factorization (PMF) factors across seven different field campaigns and find a similar composition across the more oxidized factors with about 55% acid and 26% alcohol groups. The analysis method described here can be applied to any HR-ToF-AMS data set to provide quantitative relative functional group distributions for OA mixtures.
Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .
Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .
In this article, we perform energy-dependent calculations of independent and cumulative fission product yields for 235 U, 238 U, and 239 Pu in the first chance fission region. Starting with the primary fission fragment distributions taken from available experimental data and analytical functions based on assumptions for the excitation energy and spin-parity distributions, the Hauser-Feshbach statistical decay treatment for fission fragment de-excitation is applied to more than 1,000 fission fragments for the incident neutron energies up to 5 MeV. The calculated independent yields are then used as an input of β-decay calculations to produce the cumulative yield, and summation calculations are performed. Model parameters in these procedures are adjusted by applying the Bayesian technique at the thermal energy for 235 U and 239 Pu and in the fast energy range for 238 U. The calculated fission observable quantities, such as the energy-dependent cumulative yields, and prompt and delayed neutron yields, are compared with available experimental data. We also study the possible impact of the second chance fission opening on the energy dependence of the delayed neutron yield by on the opening of second chance fission on the energy dependence calculation.
Covalent conjugation of RNA with synthetic polymers has emerged as a powerful approach for creating bioconjugates with synergistically enhanced properties. However, conventional methods require solid-phase synthesis to preinstall functional groups in RNA, significantly limiting practical applications. Here, we present a novel approach for synthesizing RNA–polymer conjugates via direct incorporation of chain transfer agent (CTA) into RNA through acylation chemistry and reversible addition–fragmentation chain transfer (RAFT) polymerization. A CTA-functionalized acyl imidazole reagent was synthesized to facilitate direct and covalent modification of various RNAs by reacting with their 2′-hydroxyl groups. Subsequent RAFT polymerization using RNA–CTA as a macro-CTA enabled direct grafting-from RNA, yielding RNA conjugates with controlled molecular weight and low dispersity. Notably, this postsynthetic modification strategy was successfully extended to modify biomass RNA, yielding thermoresponsive conjugates and biodegradable hydrogels. Overall, this advance allowed for the direct modification of synthetic and biomass RNAs, significantly enhancing the accessibility of functional RNA–polymer materials.
The problem of the quantitative description of multiscale structure in interstellar cloud complexes and gravitational collapse calculations is considered, emphasizing the recognition and characterization of hierarchical fragmentation structure. The response of the two-point correlation function to a variety of analytical models for density structure is discussed for simple clustering of pointlike clouds to more complex models involving clouds with a distribution of sizes and densities and hierarchical substructure. By expressing the density distribution as the superposition of individual clouds, it is shown that the correlation function generates two types of terms: those involving each cloud's density convolved with itself and those involving pairs of different clouds. Major distortion of the correlation function are introduced by the presence of any image features with size scales a significant fraction of the image size.
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide spatially resolved molecular information about a sample. Recently, a postionization approach (MALDI-2) has been commercially integrated with MALDI-MSI, allowing for bettered sensitivity and consequent improved spatial resolution. While advantages of MALDI-2 have previously been established, we demonstrate here statistically increased in-source fragmentation (ISF) results from postionization with a commercial instrument. Via lipid standard analyses, known MALDI ISF pathways (e.g., loss of trimethylamine) were statistically increased in MALDI-2 compared to MALDI-1 (65–172% increase in fragmentation). Gas phase molecular modeling with density functional theory estimated that the most-weighted virtual orbitals to excite within lipids involve ester and phosphate bonds. Protonated lipid excitation energies are furthermore red-shifted compared to those of other adduct types [e.g., 254 nm for protonated PC(16:0/18:1)] and approach the MALDI-2 laser energy (266 nm). Analysis of rat brain homogenate detected statistically more positive-ion mode peaks with MALDI-2 (1090) than that with MALDI-1 (719), where Kernel density estimations showed that the majority of this enhancement occurs with low m/z ions (i.e., m/z 75–500). Taken together with the lipid standard data, these observations may indicate ISF due to postionization. Finally, while artifact contributions from matrix blanks were also noted, both experimental and computational data sets suggest that the overall extent of ISF is statistically increased in MALDI-2 compared to MALDI-1.
Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828‐831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81‐83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha‐helix or beta‐sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.
Abstract Ionomers in the catalyst layer play a critical role in the performance of fuel cells and electrolyzers. Phenyl adsorption on hydrogen oxidation catalysts and electrochemical oxidation of phenyl moieties on oxygen evolution catalysts are detrimental to the alkaline devices’ performance. Here the adsorption energy of phenyl‐containing ionomers is compared to provide the rationale for implementing phenyl‐free ionomers. Density functional theory calculations indicated that the norbornane fragment has minimal adsorption energy on Pt(111) due to the absence of aromatic π electrons. A soluble quaternized polynorbornene ionomer is prepared by vinyl addition polymerization, and it exhibits high performance in both fuel cells and electrolyzers, proving the advantage of the phenyl‐free structure. This study establishes the phenyl adsorption energy‐electrode performance relationship, highlighting the importance of material interactions between the catalysts and ionomers.
Abstract Surface functionalization of two‐dimensional crystals is a key path to tuning their intrinsic physical and chemical properties. However, synthetic protocols and experimental strategies to directly probe chemical bonding in modified surfaces are scarce. Introduced herein is a mild, surface‐specific protocol for the surface functionalization of few‐layer black phosphorus nanosheets using a family of photolytically generated nitrenes (RN) from the corresponding azides. By embedding spectroscopic tags in the organic backbone, a multitude of characterization techniques are employed to investigate in detail the chemical structure of the modified nanosheets, including vibrational, X‐ray photoelectron, solid state 31 P NMR, and UV‐vis spectroscopy. To directly probe the functional groups introduced on the surface, R fragments were selected such that in conjunction with vibrational spectroscopy, 15 N‐labeling experiments, and DFT methods, diagnostic P=N vibrational modes indicative of iminophosphorane units on the nanosheet surface could be conclusively identified.
Organic components often contribute 50% or more of the submicron aerosol mass in coastal urban environments, but their partitioning between the gas and particle phases is controlled by a complex mixture of unidentified organic compounds that are poorly constrained by observations. This study compares daily filter organic functional groups (OFG) with online organic mass fragments from La Jolla, California, as part of the Eastern Pacific Cloud Aerosol Precipitation Experiment (EPCAPE), quantifying the contributions of four types of non-volatile (NV) organic emission sources to the submicron composition. Daily filters retained only 0.79–0.98 µg/m3 NV submicron organic mass concentration, even though 1.8–1.9 µg/m3 non-refractory (NR) submicron organic mass concentration was measured online. The 62–64% of measured NR submicron organic mass concentration that exceeded what remained on the filters after 23-hr sampling is interpreted as semi-volatile, consistent with the moderate correlation of the NR NV difference to NR ammonium, NR nitrate, and biomass burning-related NV and NR organic factors. The association between semi-volatile organic components and ammonium nitrate likely results from both co-emission and co-evaporation. Size-resolved filter analysis showed that NV organic mass concentration accounts for 68% of NR organic mass concentration for 0.5–1 µm dry diameter but account for 9.0% for 0.18–0.5 µm dry diameter showing the differences in volatility between particle modes. Importantly, volatility of organic components was size-dependent Information Classification: General and associated with ammonium nitrate and biomass burning, providing guidance for constraining atmospheric aerosol properties in global models.
Abstract Tidal freshwater forests were once extensive across temperate coastlines, but loss and fragmentation have made estimation of their ecosystem functions challenging. We measured water temperature for 2 years in three Sitka spruce tidal forests, a restoration site, and an adjacent emergent marsh on the Columbia River, Washington, United States. We assessed spatial variability of water temperature within sites including the effects of hydrology, differences among bay and tributary tidal forests, and differences between the tidal forests and the mainstem Columbia, the restoration site, and the emergent marsh. The tidal forests nearest to the bay had lower interior water temperatures than their channel confluences by up to 2.5°C (weekly median temperature) and 2.0°C (weekly maximum temperature), with most cooling occurring during the low‐flow months of July–September. Tributary sites had maximum temperatures up to 1.9°C cooler than bay sites and 4.2°C cooler than the mainstem. Temperatures in the two bay sites decreased by −0.16°C/100 m and −0.07°C/100 m, on average. The restoration site had the smallest within‐site temperature gradient. Differences in maximum temperatures were greatest when tidal range was low, while higher tidal ranges were associated with warmer and more variable site interiors relative to their confluences. These results suggest that water temperatures in these tidal forests can provide temperature refugia for cold water biota including salmon.
Understanding how plants perceive their environment is fundamental to advancing agricultural productivity and sustainability. Many biological small molecules, including those involved in microbial recognition, act rapidly at the plant cell surface, but the absence of tools to visualise these dynamics has limited our ability to dissect plant–microbe communication. To address this gap, we sought to create a genetically encoded biosensor that couples ligand-induced protein dimerization with the production of a fluorescent reporter. Inteins are peptide regions that excise themselves from precursor proteins and ligate the flanking chains (exteins). When each half of a split intein is fused to one of two dimerizing proteins, ligand binding brings them into proximity, inducing intein splicing and ligation of flanking extein sequences (Kang et al. 2022). Similar to previous studies, we split the yeast vacuolar ATPase subunit 1 (VMA1) intein, creating a protein biosensor that produces eGFP upon protein dimerization after ligand binding (Figure 1A) (Mootz et al. 2003). Specifically, eGFP halves (i.e., non-functional N- and C-terminal GFP fragments) were fused to the intein halves, resulting in two fusion proteins: N-terminal GFP::N-terminal intein and C-terminal intein::C-terminal GFP (Figure 1A).
The deuteron-deuteron elastic and three and four-body breakup scattering cross section have been calculated using the Faddeev-Yakubovskii (FY) chain-of-partition momentum-space equations. In this calculation the initial two-cluster potential is split into separable and non-separable components, and the effective potential is reduced to elastic two-body and three and four-body breakup open-channels and a closed-channel many-body contribution. The closed-channel contribution is determined by minimizing a variational bound. The Coulomb interaction was included by expanding the initial and final Coulomb states in a Coulomb-Sturmian basis. The three sets of chain-of-partition integral equations were solved for the elastic and three and four-body breakup scattering amplitudes. The calculations were performed for the S = 2 spin/L = 0 angular-momentum state. The elastic and double-breakup calculations were performed for energies up to E = 5.48 MeV, while the single-breakup calculations were performed for energies up to E = 4.17 MeV. In the case of elastic scattering, the calculated scattering length of 5 a dd = 7.8 ± 0.3 fm is in good agreement with a FY cluster reduction calculation. The calculated phase shift is smaller than that predicted by the resonating group model and this difference is believed to be due to the differences in the potential and calculation methods. The breakup cross sections were calculated as a function of initial deuteron momentum and fragmented-deuteron momentum. Here, the d+d → d+n+p cross sections were compared with neutron yield measurements and, while the measurements also included the L > 0 components, the general features were consistent. Estimates of the calculational uncertainties/bias are provided.
This report summarizes lower length scale computational research conducted to improve the pulverization criterion for high-burnup UO 2 fuel in the BISON fuel performance code. This research was sponsored by the NEAMS program during FY22. Efforts to improve the model primarily focus on calculating the current pressure of bubbles in the high-burnup structure (HBS) region, as well as the critical bubble pressure at which pulverization occurs in the HBS. The phase-field model for predicting initial bubble pressure in the HBS was improved by implementing a more realistic model for defect production, and by coupling the phase-field model for inter-granular bubble evolution with the spatially-resolved cluster dynamics code Xolotl to simulate intra-granular fission gas evolution. An evolution equation for current bubble pressure was added to BISON, an improvement over the previous model that assumed that bubble pressure was static following HBS formation. To improve calculations of critical bubble pressure for pulverization, 3-D phase-field fracture simulations were performed, and a function for critical bubble pressure was fit—based on the simulation results—to replace the previous function, which had been determined using 2-D simulations. The impacts of these modifications to the existing pulverization assessment cases will be reported in the forthcoming engineering scale milestone on high-burnup UO 2 pulverization. A poromechanics-based approach was used to include the effect of bubble over pressurization on the stress state of the pellet at the engineering scale, and the initial strategy for integration of the pulverization criterion with pellet-scale mechanical degradation using a smeared cracking model was developed. This report also describes the initial research that was conducted to inform a forthcoming transient fission gas release (tFGR) model in BISON. Focusing on the fission gas release caused by pulverization of the outer pellet rim, a model for the amount of fission gas release was developed as a function of fuel porosity, bubble size, and fragment size. Implementation of this model in BISON and its impact of engineering-scale predictions will also be described in the aforementioned engineering-scale milestone on high-burnup UO 2 pulverization.
Star-formation (SF) processes occurring on the scale of giant molecular clouds (10 to the 6th solar masses and 10 to the 20th cm) or smaller are discussed, reviewing the results of recent theoretical and observational investigations. Topics examined include the origin of stellar masses; bimodal SF; initial mass functions; binary stars, bound clusters, and hierarchical fragmentation; and the efficiency of SF. The properties of molecular clouds and the origin of substructures in molecular clumps are explored in detail, and consideration is given to gravitational collapse and protostars, bipolar outflows from young stellar objects, visible young stellar objects, and the implications for binary-star and planetary-system formation.