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At least 595 records · Page 33

The nature of the chemical bond

The nature of the chemical bond has long been a topic of much interest, beginning with the speculations of Isaac Newton about the “forces” that hold atoms together to the famous book by Linus Pauling with this title. For chemists, the existence of bonds between the atoms in a molecule is without question, but what are they, how can they be categorized, and what accounts for their existence? Furthermore, early theories focused on the attraction of electrical charges of opposite sign, which could account for the binding in many inorganic molecules. But what would account for the binding in electrically neutral organic molecules? Slightly more than a century ago, G. N. Lewis noted that the chemical bond appeared to be associated with electron pairs. Shortly after the discovery of the wave equation by Irwin Schrödinger in 1925-6, Heitler and London showed that quantum mechanics, in the form of what would eventually be called valence bond (VB) theory, accounted for the binding in that most improbable of molecules, the simple H 2 molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Abstract Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

Gomes-dos-Santos, André (ORCID:0000000199734861)↗

Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis

We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named "pre-op" isolates) and then 6 days later from the anastomotic site (herein named "post-op" isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown.

59 BASIC BIOLOGICAL SCIENCES↗

Fission Product Evaluation (Quarterly Report)

The LLNL team has developed a theoretical framework to compute the fission fragment charge and mass distributions of odd-mass nuclei, which can be formed in neutron-induced reactions on even-even nuclei. For example, n+ 238 U leads to the compound nucleus 239 U which has 147 neutrons. Odd-mass and odd-odd nuclei are spin-polarized: the spin of the nucleus is not equal to 0 as in even-even nuclei (a consequence of pairing correlations) but is in fact set by a single particle. In practice, that single particle can occupy different quantum-mechanical configurations, each with different spin. This affects the deformation properties of the nucleus and, as a result, the distribution of fission fragments. These distributions require two inputs for the calculation: a potential energy surface (= the total energy of the nucleus as a function of the deformation of the nuclear shape, often parametrized with 2 degrees of freedom) and the collective inertia tensor associated with each point of the PES. In an odd-mass or odd-odd nucleus, each quantity depends on the configuration of the single particle. We computed of the order of 20 to 30 different such configurations to extract the PES for spins K=1/2, 3/2, 5/2, 7/2, and 9/2 of 239 U. We then computed the primary yields for each such PES, as shown in Fig. 1 below. These yields were weighed with the spin distribution associated with the reaction 238 U+n and the resulting distribution used as input to FREYA to compute the independent yields shown in Fig. 2. These yields are then used as inputs to the FIER code to extract the cumulative yields and compare with LLNL-LANL measurements at TUNL.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Particle precipitaion into the thermosphere (invited review)

A review of research on particle precipitation into the thermosphere is presented. Particle precipitation plays an important role in thermospheric dynamics, often being both the most important ionization source and the most important heat source, comparable to Joule heating rates in the auroral zones and typically exceeding solar ultraviolet as an ionization mechanism in the nightside auroral zones and winter polar caps. Rees (1963) has shown that, roughly speaking, one electron-ion pair is produced by each 35 eV of incident electron energy flux; thus, over half of the incident electron energy flux goes into heating rather than into ionization. Precipitating ions also can produce ionization, also requiring roughly 35 eV per pair; however, since ion energy fluxes are typically much weaker than electron fluxes, they have often been neglected. The particle precipitation into the thermosphere is both an important ionization source and an important heat source; since the globally integrated value can vary over more than a factor of ten, and the instantaneous local rate can vary over nearly three orders of magnitude global, maps of precipitation rates are extremely important for predicting thermospheric weather.

Reiff, P. H.↗

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗

Role of Detuning in the Final Stage of Subharmonic Mode Transition in Boundary Layers

This work involves mechanisms for transition to turbulence in a Blasius boundary layer through resonant interactions between a plane Tollmien-Schlichting Wave and pairs of oblique waves with equal-but-opposite wave angles. When the frequency of the TS wave is exactly twice that of the oblique waves, we have a "tuned" subharmonic resonance. This leads to the enhanced growth of the oblique modes. Following this, other nonlinear interactions lead to the growth of other 3-D modes which are harmonically based, along with a 3-D mean flow distortion. In the final stage of this process, a gradual spectral filling occurs which we have traced to the growth of fundamental and subharmonic side-band modes. To simulate this with controlled inputs, we introduced the oblique wave pairs at the same conditions, but shifted the frequency of the plane TS mode (by as much as 12 percent) so that it was not exactly twice that of the 3-D modes. These "detuned" conditions also lead to the enhanced growth of the oblique modes, as well as discrete side-band modes which come about through sum and difference interactions. Other interactions quickly lead to a broad band of discrete modes. Of particular importance is the lowest difference frequency which produces a low frequency modulation similar to what has been seen in past experiments with natural 3-D mode input. Cross-bispectral analysis of time series allows us to trace the origin and development of the different modes. Following these leads to a scenario which we believe is more relevant to conditions of "natural" transitions, where low amplitude background disturbances either lead to the gradual detuning of exact fundamental/subharmonic resonance, or in which 3-D mode resonance is detuned from the onset. The results contrast the two conditions, and document the propensity of the 2-D/3-D mode interactions to become detuned.

Corke, Thomas C.↗

Quantifying the Importance of Selected Drought Indicators for the United States Drought Monitor

Using information theory, our study quantifies the importance of selected indicators for the U.S. Drought Monitor (USDM) maps. We use the technique of mutual information (MI) to measure the importance of any indicator to the USDM, and because MI is derived solely from the data, our findings are independent of any model structure (conceptual, physically-based, or empirical). We also compare these MIs against the drought representation effectiveness ratings in the North America Drought Indices and Indicators Assessment (NADIIA) survey for Koeppen climate zones. This reveals: [1] agreement between some ratings and our MI values (high for example indicators like Standardized Precipitation-Evapotranspiration Index or SPEI); [2] some divergences (for example, soil moisture has high ratings but near-zero MIs for ESA-CCI soil moisture in the Western U.S., indicating the need of another remotely sensed soil moisture source); and [3] new insights into the importance of variables such as Snow Water Equivalent (SWE) that are not included in sources like NADIIA. Further analysis of the MI results yields findings related to: [1] hydrological mechanisms (summertime SWE domination during individual drought events through snowmelt into the water-scarce soil); [2] hydroclimatic types (the top pair of inputs in the Western and non-Western regions are SPEIs and soil moistures respectively); and [3] predictability (high for the California 2012-2017 event, with longer-timescale indicators dominating). Finally, the high MIs between multiple indicators jointly and the USDM indicate potentially high drought forecasting accuracies achievable using only model-based inputs, and the potential for global drought monitoring using only remotely sensed inputs, especially for locations having insufficient in situ observations.

Drought↗

Analysis of Thermoradiative Thermal Energy Conversion

The thermoradiative cell is a new method for converting heat energy to electrical power, first detailed by Strandberg in 2015. The cell is a p-n junction semiconductor device, similar to a photovoltaic cell but thermodynamically operating in the reverse direction, converting the thermal dark current into electrical power while radiating waste heat to space. The power and efficiency can be calculated as a function of bandgap in the Shockley-Queisser detailed-balance limit, in which the thermal emissivity of the cell is due to the recombination of electron-hole pairs, and all other recombination losses are ignored. The current produced is directly proportional to the recombination radiation. The fundamental loss mechanism for the thermoradiative cell is the energy carried by the infrared radiation into space from band-to-band recombination of carriers injected across the junction. In an ideal cell, to maximize the efficiency, the emission energy of these photons would precisely equal the bandgap. This can be achieved, for example, using dielectric filters or meta-material filters to recycle emission at other wavelengths back into the cell. The voltage is proportional to the external bias. These two constraints allow optimization of the optimum bias point for maximum power. Unlike photovoltaic cells, the maximum power operating point is not the same as the maximum efficiency point, and higher efficiency can be achieved at a higher (negative) bias in the ideal case. Incorporating non-ideal losses, however, shifts the maximum efficiency point toward lower bias. Unlike in photovoltaic cells, non-radiative recombination (e.g., Auger losses) will reduce the output current, but will not reduce the conversion efficiency, since the recombination energy is retained in the cell in the form of heat. Since a thermoradiative cell operates by radiating directly to space, the current produced by themoradiative cells will increase as Stefan-Boltzmann radiation; roughly the fourth power of the temperature. Thus, the power produced is highest at high operating temperatures, and, unlike conventional thermal conversion, increasing radiator temperature increases, the efficiency. Thus, the choice of technology will be toward semiconductors resistant to degradation at high temperature.

Thermoradiative↗

Initial Motor Winding Insulation Lifetime Experimental Results for Electric Aircraft Applications

Electric and hybrid-electric aircraft require high-performance and reliable electric motors to meet aviation performance and safety requirements. One of the most common failure mechanisms in electric motors is winding insulation breakdown. In this paper, initial set of aging experiments are carried out on twisted pairs and motorette specimens. The twisted pairs are aged with multiple steady-temperature thermal aging cycles. The motorette specimens are thermally cycled by applying current to the windings. Partial discharge inception voltage is tracked and reported throughout the aging process. The end goal of this work is to develop methods and models for assessing the lifetime of motor winding insulation in electric and hybrid electric aircraft applications.

Thomas Tallerico↗

Thermodynamics and Mechanism of a Photocatalyzed Stereoselective [2 + 2] Cycloaddition on a CdSe Quantum Dot

Colloidal quantum dots (QDs) have shown promise over the last few decades for a range of applications including single photon emission, in vivo imaging and photocatalysis. Recent experiments demonstrated that QDs impart stereoselectivity to triplet excited-state [2+2] cycloaddition reactions of alkenes photocatalyzed by the QD through self-assembly of the reagent molecules on the QD surface, but these experiments did not reveal the precise geometries of surface-bound molecules or their interactions with surface atoms. Here, a theoretical mechanistic approach is used to study such interactions for [2+2] cycloadditions of 4-vinylbenzoic acid derivatives on CdSe QDs. Spin-polarized periodic density functional theory (DFT) and non-periodic DFT calculations are deployed to determine the origin of the selectivity for the syn diastereomer of the resultant tetrasubstituted cyclobutane product via atomistic modelling of the CdSe surface and substrates, and determination of the thermodynamic energies of reactions for each step, the intermolecular interactions between the substrates, and the triplet state reaction paths. The calculations indicate that reaction selectivity arises from preferred binding of pairs through intermolecular interactions of substrate molecules on the QD surface in a syn-precursor structure followed by dimerization after triplet excitation. Further, these mechanisms are generalizable to other metal-enriched QD surfaces that have a similar surface structure to CdSe, such as InSe or CdTe. Design principles for anti diastereomer derivatives are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Valuing EV Managed Charging for Bulk Power Systems

When and where electric vehicle (EV) charging occurs has significant implications for power systems supporting widespread EV adoption, especially with high shares of wind and solar generation. This study extends previous works by leveraging detailed simulation models for EV adoption, EV use, EV charging, and bulk power system operations, and by linking them with methods for describing charging flexibility at both the individual vehicle and aggregate levels. This technical potential study focuses on how the value of EV managed charging (EVMC) changes depending on charging flexibility type (within-charging session or within-week scheduling), dispatch mechanism (direct load control or one of several price-based mechanisms), and managed charging participation rate. We show that naively aggregating EV charging flexibility from individual vehicles into megawatt-scale resources grossly overestimates the flexibility of the fleet, because such aggregate models can unrealistically pair, e.g., one already-fully-charged vehicle's ability to increase load with another already-charging vehicle's ability to accept more charge, effectively requesting a charging rate that is infeasible for the latter vehicle. We find per-vehicle bulk system value is highest at low participation rates for all dispatch mechanisms. Factoring in production cost savings, avoided firm capacity savings, and combustion-related power sector emissions savings, we estimate the value of EVMC at low participation rates (5%) to be $33/vehicle-year to $69/vehicle-yr for within-session charging flexibility and $40/vehicle-yr to $120/vehicle-yr for within-week charging flexibility in an envisioned 2038 New England power system and monetary value reported in 2016 U.S. dollars. At 100% participation, per-vehicle value declines to $25/vehicle-yr to $31/vehicle-yr for within-session charging flexibility and to $29/vehicle-yr to $36/vehicle-yr for within-week charging flexibility; however, 100% participation yields the highest total system savings.

ADVANCED PROPULSION SYSTEMS↗

Long, paired A'A/Pahoehoe flows of Mauna Loa: Volcanological significance and insights they provide into volcano plumbing systems

The long lava flows of Mauna Loa, Hawaii have been cited as Earth's closed analogs to the large Martian flows. It is therefore important to understand the flow mechanics and characteristics of the Mauna Loa flows and to make use of these in an attempt to gain insights into Martian eruptive processes. Two fundamentally different kinds of long lava flows can be distinguished on Hawaiian volcanoes as in Martian flows. The two kinds may have identical initial viscosities, chemical compositions, flow lengths, and flow volumes, but their flow mechanisms and thermal energy budgets are radically different. One travels a distance set by the discharge rate as envisaged by Walker and Wadge, and the other travels a distance set mainly by the eruption duration and ground slope. In the Mauna Loa lavas, yield strength becomes an important flow morphology control only in the distal part of a'a lavas. The occurrence of paired flows on Mauna Loa yields insights into the internal plumbing systems of the volcano, and it is significant that all of the volume of the a'a flow must be stored in a magma chamber before eruption, while none of the volume of the pahoehoe needs to be so stored. Differentiation between the two kinds of flows on images of Martian volcanoes is possible and hence an improved understanding of these huge structures is acquired.

Rowland, Scott K.↗

Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity

Metabolic reprogramming, including increased glucose uptake and lactic acid excretion, is a hallmark of cancer. The glycolytic ‘gatekeeper’ enzyme phosphofructokinase-1 (PFK1), which catalyzes the step committing glucose to breakdown, is dysregulated in cancers. While altered PFK1 activity and expression in tumors have been demonstrated, little is known about the effects of cancer-associated somatic mutations. Somatic mutations in PFK1 inform our understanding of allosteric regulation by identifying key amino acid residues involved in the regulation of enzyme activity. Here, we characterized mutations disrupting an evolutionarily conserved salt bridge between aspartic acid and arginine in human platelet (PFKP) and liver (PFKL) isoforms. Using purified recombinant proteins, we showed that disruption of the Asp–Arg pair in two PFK1 isoforms decreased enzyme activity and altered allosteric regulation. We determined the crystal structure of PFK1 to 3.6 Å resolution and used molecular dynamic simulations to understand molecular mechanisms of altered allosteric regulation. We showed that PFKP-D564N had a decreased total system energy and changes in the electrostatic surface potential of the effector site. Cells expressing PFKP-D564N demonstrated a decreased rate of glycolysis, while their ability to induce glycolytic flux under conditions of low cellular energy was enhanced compared with cells expressing wild-type PFKP. Taken together, these results suggest that mutations in Arg–Asp pair at the interface of the catalytic-regulatory domains stabilizes the t-state and presents novel mechanistic insight for therapeutic development in cancer.

59 BASIC BIOLOGICAL SCIENCES↗

Search for neutrino lines from dark matter annihilation and decay with IceCube

Dark matter particles in the Galactic Center and halo can annihilate or decay into a pair of neutrinos producing a monochromatic flux of neutrinos. The spectral feature of this signal is unique and it is not expected from any astrophysical production mechanism. Its observation would constitute a dark matter smoking gun signal. Here we performed the first dedicated search with a neutrino telescope for such signal, by looking at both the angular and energy information of the neutrino events. To this end, a total of five years of IceCube’s DeepCore data has been used to test dark matter masses ranging from 10 GeV to 40 TeV. No significant neutrino excess was found and upper limits on the annihilation cross section, as well as lower limits on the dark matter lifetime, were set. The limits reached are of the order of 10 -24 cm 3 /s for an annihilation and up to 10 27 s for decaying dark matter. Using the same data sample we also derive limits for dark matter annihilation or decay into a pair of Standard Model charged particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantum Pair Generation in Nonlinear Metasurfaces with Mixed and Pure Photon Polarizations

Metasurfaces are highly effective at manipulating classical light in the linear regime; however, effectively controlling the polarization of nonclassical light generated from nonlinear resonant metasurfaces remains a challenge. Here, in this study, we present a solution by achieving polarization engineering of frequency-nondegenerate biphotons emitted via spontaneous parametric down-conversion in GaAs metasurfaces, utilizing quasi-bound states in the continuum (qBIC) resonances to enhance biphoton generation. Through comprehensive polarization tomography, we demonstrate that the emitted photons’ polarization directly reflects the qBIC mode’s far-field properties. Furthermore, we show that both the type of qBIC mode and the symmetry of the meta-atoms can be tailored to control each single-photon polarization state, and that the subsequent two-photon polarization states are nearly separable, offering potential applications in the heralded generation of single photons with adjustable polarization. This work provides a significant step toward utilizing metasurfaces to generate quantum light and engineer their polarization, a critical aspect for future quantum technologies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Ion Pairing and Redissociaton in Low-Permittivity Electrolytes for Multivalent Battery Applications

Detailed speciation of electrolytes as a function of chemical system and concentration provides the foundation for understanding bulk transport as well as possible decomposition mechanisms. In particular, multivalent electrolytes have shown a strong coupling between anodic stability and solvation structure. Furthermore, solvents that are found to exhibit reasonable stability against alkaline-earth metals generally exhibit low permittivity, which typically increases the complexity of the electrolyte species. To improve our understanding of ionic population and associated transport in these important classes of electrolytes, the speciation of Mg(TFSI)2 in monoglyme and diglyme systems is studied via a multiscale thermodynamic model using first-principles calculations for ion association and molecular dynamics simulations for dielectric properties. The results are then compared to Raman and dielectric relaxation spectroscopies, which independently confirm the modeling insights. We find that the significant presence of free ions in the low-permittivity glymes in the concentration range from 0.02 to 0.6 M is well-explained by the low-permittivity redissociation hypothesis. Here, salt speciation is largely dictated by long-range electrostatics, which includes permittivity increases due to polar contact ion pairs. The present results suggest that other low-permittivity multivalent electrolytes may also reach high conductivities as a result of redissociation.

25 ENERGY STORAGE↗