Interaction between Hydrated Smectite Clay Particles as a Function of Salinity (0–1 M) and Counterion Type (Na, K, Ca)
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11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
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High Field Transport in (Ultra) Wide Bandgap Semiconductors: Diamond Versus Cubic GaN
We provide an analysis of nonlinear transport in diamond and cubic GaN (c-GaN) with emphasis on the different types of optical phonon scattering [i.e., optical deformation potential (ODP) scattering versus polar optic phonon (POP) scattering] limiting the carrier velocity. Both types of carrier mobilities and carrier saturation (peak) velocities in diamond and c-GaN as functions of different doping types and concentrations are obtained by directly solving the Boltzmann equation. Our model indicates that the nonrandomizing nature of POP scattering causes carrier temperature cooling, resulting in higher carrier drift velocity than with ODP scattering. This effect, in addition to the small carrier effective masses and large optical phonon energies, is responsible for the higher peak velocities in c-GaN, compared to carrier drift velocity in diamond.
42 ENGINEERING↗
Observation of Polarization-Dependent Changes in Higher-Order Mode Responses as a Function of Transverse Beam Position in Tesla-Type Cavities at FAST
Higher-order modes (HOMs) in superconducting rf cavities present problems for an electron bunch traversing the cavity in the form of long-range wakefields from previous bunches. These may dilute the emittance of the macropulse average, especially with low emittance beams at facilities such as the European X-ray Free-electron Laser (XFEL) and the upgraded Linac Coherent Light Source (LCLS-II). Here we present observations of HOMs driven by the beam at the Fermilab Accelerator Science and Technology (FAST) facility. The FAST facility features two independent TESLA-type cavities (CC1 and CC2) after a photocathode rf gun followed by an 8-cavity cryomodule. The HOM signals were acquired from cavities using bandpass filters of 1.75 ± 0.15 GHz, 2.5 ± 0.2 GHz, and 3.25 ± 0.2 GHz and recorded using an 8-GHz, 20 GSa/s oscilloscope. The frequency resolution obtained is sufficient to separate polarization components of many of the HOMs. These HOM signals were captured from CC1 and cavities 1 and 8 of the cryomodule for various initial trajectories through the cavities, and we observe correlations between trajectory, HOM signals, and which polarization component of a mode is affected.
Thurman-Keup, Randy Michael↗
Observation of Polarization-Dependent Changes in Higher Order Mode Responses as a Function of Transverse Beam Position in TESLA-Type Cavities at FAST
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Thurman-Keup, Randy Michael↗
The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks
Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type.
cell specificity↗
Spatiotemporal metabolic responses to water deficit stress in distinct leaf cell-types of poplar
The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, plant tissues are made of several distinct cell types with unique and differentiated functions, which limits whole tissue ‘omics’-based studies to determine only an averaged molecular signature arising from multiple cell types. Advancements in spatial omics technologies provide an opportunity to understand the molecular mechanisms underlying plant responses to WD stress at distinct cell-type levels. Here, we studied the spatiotemporal metabolic responses of two poplar ( Populus tremula× P. alba ) leaf cell types -palisade and vascular cells- to WD stress using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified unique WD stress-mediated metabolic shifts in each leaf cell type when exposed to early and prolonged WD stresses and recovery from stress. During water-limited conditions, flavonoids and phenolic metabolites were exclusively accumulated in leaf palisade cells. However, vascular cells mainly accumulated sugars and fatty acids during stress and recovery conditions, respectively, highlighting the functional divergence of leaf cell types in response to WD stress. By comparing our MALDI-MSI metabolic data with whole leaf tissue gas chromatography-mass spectrometry (GC-MS)-based metabolic profile, we identified only a few metabolites including monosaccharides, hexose phosphates, and palmitic acid that showed a similar accumulation trend at both cell-type and whole leaf tissue levels. Overall, this work highlights the potential of the MSI approach to complement the whole tissue-based metabolomics techniques and provides a novel spatiotemporal understanding of plant metabolic responses to WD stress. This will help engineer specific metabolic pathways at a cellular level in strategic perennial trees like poplars to help withstand future aberrations in environmental conditions and to increase bioenergy sustainability.
59 BASIC BIOLOGICAL SCIENCES↗
HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160
HVEM is a TNF (tumor necrosis factor) receptor contributing to a broad range of immune functions involving diverse cell types. It interacts with a TNF ligand, LIGHT, and immunoglobulin (Ig) superfamily members BTLA and CD160. Assessing the functional impact of HVEM binding to specific ligands in different settings has been complicated by the multiple interactions of HVEM and HVEM binding partners. To dissect the molecular basis for multiple functions, we determined crystal structures that reveal the distinct HVEM surfaces that engage LIGHT or BTLA/CD160, including the human HVEM–LIGHT–CD160 ternary complex, with HVEM interacting simultaneously with both binding partners. Based on these structures, we generated mouse HVEM mutants that selectively recognized either the TNF or Ig ligands in vitro. Knockin mice expressing these muteins maintain expression of all the proteins in the HVEM network, yet they demonstrate selective functions for LIGHT in the clearance of bacteria in the intestine and for the Ig ligands in the amelioration of liver inflammation.
60 APPLIED LIFE SCIENCES↗
Understanding the Chemomechanical Function of the Silver–Carbon Interlayer in Sheet-type All-Solid-State Lithium–Metal Batteries
All-solid-state batteries with lithium metal anodes hold great potential for high-energy battery applications. However, forming and maintaining stable solid–solid contact between the lithium anode and solid electrolyte remains a major challenge. One promising solution is the use of a silver–carbon (Ag–C) interlayer, but its chemomechanical properties and impact on interface stabilities need to be comprehensively explored. Here, we examine the function of Ag–C interlayers in addressing interfacial challenges using various cell configurations. Experiments show that the interlayer improves interfacial mechanical contact, leading to a uniform current distribution and suppressing lithium dendrite growth. Furthermore, the interlayer regulates lithium deposition in the presence of Ag particles via improved Li diffusivity. The sheet-type cells with the interlayer achieve a high energy density of 514.3 Wh L –1 and an average Coulombic efficiency of 99.97% over 500 cycles. Furthermore, this work provides insights into the benefits of using Ag–C interlayers for enhancing the performance of all-solid-state batteries.
25 ENERGY STORAGE↗
Direct evidence of low work function on SrVO 3 cathode using thermionic electron emission microscopy and high-field ultraviolet photoemission spectroscopy
Perovskite SrVO 3 has recently been proposed as a novel electron emission cathode material. Density functional theory (DFT) calculations suggest multiple low work function surfaces, and recent experimental efforts have consistently demonstrated effective work functions of ~2.7 eV for polycrystalline samples, both results suggesting, but not directly confirming, that some fraction of even lower work function surface is present. In this work, thermionic electron emission microscopy (ThEEM) and high-field ultraviolet photoemission spectroscopy (UPS) are used to study the local work function distribution and measure the work function of a partially oriented- (110)-SrVO 3 perovskite oxide cathode surface. Our results show direct evidence of low work function patches of about 2.0 eV on the cathode surface, with a corresponding onset of observable thermionic emission at 750 °C. We hypothesize that, in our ThEEM and UPS experiments, the high applied electric field suppresses the patch field effect, enabling the direct measurement of local work functions. This measured work function of 2.0 eV is comparable to the previous DFT-calculated work function values of the SrVO-terminated (110) SrVO 3 surface (2.3 eV) and SrO-terminated (100) surface (1.9 eV). The measured 2.0 eV value is also much lower than the work function for the (001) LaB 6 single crystal cathode (~2.7 eV) and comparable to the effective work function of B-type dispenser cathodes (~2.1 eV). If SrVO 3 thermionic emitters can be engineered to access domains of this low 2.0 eV work function, they have the potential to significantly improve thermionic emitter-based technologies.
36 MATERIALS SCIENCE↗
Halophytes and heavy metals: A multi‐omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima
Abstract Premise The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we usedCakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole‐genome triplication with closely related salt‐sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. Methods Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response inC. maritimaand identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. Results Cakile maritimais tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool inC. maritimaand likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved inC. maritimaabiotic stress tolerance. Conclusions These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.
Plant Sciences↗
Perennial grass root system specializes for multiple resource acquisitions with differential elongation and branching patterns
Roots optimize the acquisition of limited soil resources, but relationships between root forms and functions have often been assumed rather than demonstrated. Furthermore, how root systems co-specialize for multiple resource acquisitions is unclear. Theory suggests that trade-offs exist for the acquisition of different resource types, such as water and certain nutrients. Measurements used to describe the acquisition of different resources should then account for differential root responses within a single system. To demonstrate this, we grew Panicum virgatum in split-root systems that vertically partitioned high water availability from nutrient availability so that root systems must absorb the resources separately to fully meet plant demands. We evaluated root elongation, surface area, and branching, and we characterized traits using an order-based classification scheme. Plants allocated approximately 3/4th of primary root length towards water acquisition, whereas lateral branches were progressively allocated towards nutrients. However, root elongation rates, specific root length, and mass fraction were similar. Our results support the existence of differential root functioning within perennial grasses. Similar responses have been recorded in many plant functional types suggesting a fundamental relationship. Root responses to resource availability can be incorporated into root growth models via maximum root length and branching interval parameters.
59 BASIC BIOLOGICAL SCIENCES↗
Deep Kronecker neural networks: A general framework for neural networks with adaptive activation functions
Here we propose a new type of neural networks, Kronecker neural networks (KNNs), that form a general framework for neural networks with adaptive activation functions. KNNs employ the Kronecker product, which provides an efficient way of constructing a very wide network while keeping the number of parameters low. Our theoretical analysis reveals that under suitable conditions, KNNs induce a faster decay of the loss than that by the feed-forward networks. This is also empirically verified through a set of computational examples. Furthermore, under certain technical assumptions, we establish global convergence of gradient descent for KNNs. As a specific case, we propose the Rowdy activation function that is designed to get rid of any saturation region by injecting sinusoidal fluctuations, which include trainable parameters. The proposed Rowdy activation function can be employed in any neural network architecture like feed-forward neural networks, Recurrent neural networks, Convolutional neural networks etc. The effectiveness of KNNs with Rowdy activation is demonstrated through various computational experiments including function approximation using feed-forward neural networks, solution inference of partial differential equations using the physics-informed neural networks, and standard deep learning benchmark problems using convolutional and fully-connected neural networks.
97 MATHEMATICS AND COMPUTING↗
Growth functions of periodic space tessellations
This work analyzes the rules governing the growth of the numbers of vertices, edges and faces in all possible periodic tessellations of the 2D Euclidean space, and encodes those rules in several types of polynomial growth functions. These encodings map the geometric, combinatorial and topological properties of the tessellations into sets of integer coefficients. Several general statements about these encodings are given with rigorous mathematical proof. The variation of the growth functions is represented graphically and analyzed in orphic diagrams, so named because of their similarity to orphic art. Several examples of 3D space groups are included, to emphasize the complexity of the growth functions in higher dimensions. A freely available Python library is presented to facilitate the discovery of the growth functions and the generation of orphic diagrams.
Chemistry↗
RRNPP-type quorum-sensing systems regulate solvent formation, sporulation and cell motility in Clostridium saccharoperbutylacetonicum
Abstract Background Clostridium saccharoperbutylacetonicum N1-4 (HMT) is a strictly anaerobic, spore-forming Gram-positive bacterium capable of hyper-butanol production through the well-known acetone–butanol–ethanol fermentation process. Recently, five putative RRNPP-type QSSs (here designated as QSS1 to QSS5) were predicted in this bacterial strain, each of which comprises a putative RRNPP-type regulator (QssR1 to QssR5) and a cognate signaling peptide precursor (QssP1 to QssP5). In addition, both proteins are encoded by the same operon. The functions of these multiple RRNPP-type QSSs are unknown. Results To elucidate the function of multiple RRNPP-type QSSs as related to cell metabolism and solvent production in N1-4 (HMT), we constructed qssR -deficient mutants ΔR1, ΔR2, ΔR3 and ΔR5 through gene deletion using CRISPR–Cas9 and N1-4-dcas9-R4 (with the QssR4 expression suppressed using CRISPR–dCas9). We also constructed complementation strains by overexpressing the corresponding regulator gene. Based on systematic characterization, results indicate that QSS1, QSS2, QSS3, and QSS5 positively regulate the sol operon expression and thus solvent production, but they likely negatively regulate cell motility. Consequently, QSS4 might not directly regulate solvent production, but positively affect cell migration. In addition, QSS3 and QSS5 appear to positively regulate sporulation efficiency. Conclusions Our study provides the first insights into the roles of multiple RRNPP-type QSSs of C. saccharoperbutylacetonicum for the regulation of solvent production, cell motility, and sporulation. Results of this study expand our knowledge of how multiple paralogous QSSs are involved in the regulation of essential bacterial metabolism pathways.
09 BIOMASS FUELS↗
Amine-functionalized porous organic polymers for carbon dioxide capture
Recent developments in CO 2 capture using porous organic polymers (POPs) have received accrescent attention due to their sorbent properties such as high CO 2 uptake capacity and selectivity, tunable chemical structure and permanent porosity. POPs are constructed using two and/or three-dimensional organic monomers (building blocks) linked to each other through covalent bonding, creating high porosity. The pore structure in POPs is exceptionally stable, which leads to their cyclable CO 2 adsorption performance. However, POPs generally suffer from low CO 2 uptake and selectivity due to their interaction with CO 2 in physisorption limits (20–40 kJ mol -1 ). Similar to that in other physisorbents, the CO 2 uptake capacity of POPs further decreases under humid conditions. Pursuant to these limitations, amine functionalization in POPs has resulted in enhanced CO 2 uptake performance with improved CO 2 selectivity over non-polar gases such as N 2 . More importantly, several types of amine-functionalized POPs showed that the CO 2 uptake could remain intact under humid conditions such as in post-combustion flue gas. This review article covers recent developments in amine-functionalized porous organic polymers. Three main categories of amine functionalization, such as direct amine synthesis, amine impregnation and amine grafting, were investigated in detail by considering the effect of amines on the sorbent properties and CO 2 capture performance of POPs. The recent findings in amine-functionalized POPs were investigated including porous polymeric networks (PPNs), covalent organic frameworks (COFs), amine linked POPs, hyper-crosslinked polymers (HCPs), conjugated microporous polymers (CMPs), benzimidazole linked polymers (BILPs), porous aromatic frameworks (PAFs) and polymers of intrinsic microporosity (PIMs).
36 MATERIALS SCIENCE↗
SpectrumSDT: A program for parallel calculation of coupled rotational-vibrational energies and lifetimes of bound states and scattering resonances in triatomic systems
In this work, we present SpectrumSDT – a program for calculations of energies and lifetimes of bound rotational-vibrational states below and scattering resonances above the dissociation threshold on a global potential energy surface of a triatomic system, which may include stable molecules, weekly-bound van-der-Waals complexes, and unbound atom + diatom scattering systems. Large-amplitude vibrational motion is treated explicitly using hyper-spherical coordinates. Three options for the rotational-vibrational interaction are supported: uncoupled (symmetric top rotor), partially coupled (to include interaction between several nearest states only) and full-coupled (vibrating asymmetric-top rotor). In addition to energies and lifetimes, SpectrumSDT is able to integrate ro-vibrational wave functions over the user-defined regions of potential energy surface, which helps to classify these states. In this release of the code, SpectrumSDT is limited to ABA-type molecules with wave functions that do not extend into the regions near Eckart singularities.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Extreme confinement of hydrogen gas within fullerenelike nanoporous carbon
Nanoporous carbons and carbon nanostructures can store hydrogen at cryogenic temperatures but lack the volumetric and gravimetric capacity to be industrially significant. Recent inelastic neutron scattering experiments suggest a highly dense phase of hydrogen at temperatures well above the melting point of solid hydrogen. However, it remains unclear how pore geometry and intermolecular interactions enable these dense phases to exist, with dispersion (van der Waals) or electrostatic/induction suggested to be the key effects in slit and curved pores but their relative contributions have yet to be quantified. In this paper, we perform benchmark electronic structure calculations allowing the interactions between planar and curved aromatic molecules with hydrogen to be accurately determined. Dispersion was found to dominate over electrostatic and inductive effects with some many-body charge transfer (Dobson type-A) effects needed to capture the most highly curved structures. Density functional methods that include type-A many-body effects were found to accurately describe the intermolecular interactions at a fraction of the cost of coupled-cluster simulations and these approaches were used to calculate the energies inside large carbon bowl and slit pores. The interaction energies inside the bowl pores were found to depend on the orientation of the hydrogen molecule. This rotational barrier, modeled as a quantum hindered rotor, could reproduce the peak splitting observed in inelastic neutron scattering experiments, with weak splitting arising from bowl-like fullerene pores and strong splitting from highly confining nanotubelike pores. Increasing the fraction of such curved pores in nanoporous carbons may therefore offer a pathway to enhance their hydrogen-storage capacity. Moreover, the preferential adsorption of ortho hydrogen on nanotubelike pores could enable the storage of high-density hydrogen without the need to remove heat produced during the ortho-para hydrogen conversion.
36 MATERIALS SCIENCE↗
Higher-order SPOP assembly reveals a basis for cancer mutant dysregulation
The speckle-type POZ protein (SPOP) functions in the Cullin3-RING ubiquitin ligase (CRL3) as a receptor for the recognition of substrates involved in cell growth, survival, and signaling. SPOP mutations have been attributed to the development of many types of cancers, including prostate and endometrial cancers. Prostate cancer mutations localize in the substrate-binding site of the substrate recognition (MATH) domain and reduce or prevent binding. However, most endometrial cancer mutations are dispersed in seemingly inconspicuous solvent-exposed regions of SPOP, offering no clear basis for their cancer-causing and peculiar gain-of-function properties. Herein, we present the first structure of SPOP in its oligomeric form, uncovering several new interfaces important for SPOP self-assembly and normal function. Given that many previously unaccounted-for cancer mutations are localized in these newly identified interfaces, we uncover molecular mechanisms underlying dysregulation of SPOP function, with effects ranging from gross structural changes to enhanced self-association, and heightened stability and activity.
59 BASIC BIOLOGICAL SCIENCES↗