Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry
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Castro‐Torres, Eduardo↗
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The Industry Energy Tool (IET): Documentation
Studies of industrial energy use typically mention the sector's heterogeneity and complexity as modelling barriers. One of the more significant impediments to analyzing and building models of U.S. industrial energy use is the lack of current, disaggregated data. The Industry Energy Tool (IET) and its foundational data addresses some of these barriers. The IET uses county-level energy data with stock turnover, energy efficiency, fuel switching, and emissions functionalities to calculate energy use and emissions from agriculture, construction, mining, and manufacturing industries from 2014 to 2050. The IET is an open-source, transparent, and flexible tool for exploring industrial sector energy and emissions scenarios. The IET takes a simplified approach to developing scenario projections of energy and emissions by allowing users to modify pre-populated inputs for achieved energy efficiency, rate of equipment stock turnover, and future penetration renewable electricity. In addition to its transparency and flexibility, the strengths of the IET lie in its geographically- and operationally-disaggregated data set. The IET's foundational data is built on energy data first calculated at the facility- and technology-level for many of the largest energy-using industries. These data are then aggregated to the county and end-use level with other publicly-available data for use in scenarios estimated by the IET.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Tuning anisotropic bonding via chemistry and pressure in layered pnictides and chalcogenides (Final Report)
The overarching goal of this research program, as originally delineated in the proposal “Tuning anisotropic bonding via chemistry and pressure in layered pnictides and chalcogenides” was to develop a predictive, chemistry-driven understanding of the impact of the phonon behavior on thermal properties of bulk layered materials. At finite temperatures, atomic vibrations (phonons) strongly impact the thermodynamics, thermal and electrical transport, and phase-switching properties of functional materials. In particular, soft phonon modes and strongly anharmonic potentials can have spectacular consequences, including structural phase transitions (for example in ferroelectrics and phase-change memory materials), metal-insulator transitions, and extreme thermal resistance preventing heat propagation. Bulk materials with highly-anisotropic bonding may provide unique strategies to induce soft-phonon modes and lattice instabilities. Recently, increasingly detailed investigations of the lattice dynamics in layered materials have been made possible by the advent of first-principles phonon calculations and advanced characterization techniques based on neutron and X-ray scattering. However, due to the lack of studies in which composition and bonding character are systematically varied, there are still fundamental questions regarding the impacts of anisotropic bonding and anharmonicity on lattice stability and thermal transport. One of the major goals of this research program is therefore to address this gap by coherently tuning bonding anisotropy and anharmonicity across families of related compounds. Such approaches have revealed new strategies for exploiting structural anisotropy in quasi-1D and 2D bulk materials to obtain tailored functional properties. This project systematically explored the lattice dynamics, phase stability, and transport properties in bulk layered materials by using both composition and applied pressure to tune the degree of bonding anisotropy and anharmonicity. To accomplish this work, we combined i) single-crystal growth of key material systems with tunable anisotropy, ii) in-situ high-temperature/high-pressure characterization of structure and phonons to probe bonding anisotropy and anharmonicity, including state-of-the-art inelastic X-ray scattering (IXS) and inelastic neutron scattering (INS), and iii) first-principles simulations leveraging large-scale computing to identify the fundamental origins of the observed effects, by relating atomic structure and dynamics to electronic orbital interactions. Finally, we modeled and verified the impact of the phonon behavior on thermal transport to identify new strategies for a-priori design of thermal conductivity. Our integrated collaborative approach helped to systematically unravel the effects of anisotropy and bonding anharmonicity on phonon transport, thermodynamics, and thermal properties of complex anisotropic materials.
30 DIRECT ENERGY CONVERSION↗
Tuning anisotropic bonding via chemistry and pressure in layered pnictides and chalcogenides. Final Report
The overarching goal of this research program, as originally delineated in the proposal “Tuning anisotropic bonding via chemistry and pressure in layered pnictides and chalcogenides” was to develop a predictive, chemistry-driven understanding of the impact of the phonon behavior on thermal properties of bulk layered materials. At finite temperatures, atomic vibrations (phonons) strongly impact the thermodynamics, thermal and electrical transport, and phase-switching properties of functional materials. In particular, soft phonon modes and strongly anharmonic potentials can have spectacular consequences, including structural phase transitions (for example in ferroelectrics and phase-change memory materials), metal-insulator transitions, and extreme thermal resistance preventing heat propagation. Bulk materials with highly-anisotropic bonding may provide unique strategies to induce soft-phonon modes and lattice instabilities. Recently, increasingly detailed investigations of the lattice dynamics in layered materials have been made possible by the advent of first-principles phonon calculations and advanced characterization techniques based on neutron and X-ray scattering. However, due to the lack of studies in which composition and bonding character are systematically varied, there are still fundamental questions regarding the impacts of anisotropic bonding and anharmonicity on lattice stability and thermal transport. One of the major goals of this research program is therefore to address this gap by coherently tuning bonding anisotropy and anharmonicity across families of related compounds. Such approaches have revealed new strategies for exploiting structural anisotropy in quasi-1D and 2D bulk materials to obtain tailored functional properties. This project systematically explored the lattice dynamics, phase stability, and transport properties in bulk layered materials by using both composition and applied pressure to tune the degree of bonding anisotropy and anharmonicity. To accomplish this work, we combined i) single-crystal growth of key material systems with tunable anisotropy, ii) in-situ high-temperature/high-pressure characterization of structure and phonons to probe bonding anisotropy and anharmonicity, including state-of-the-art inelastic X-ray scattering (IXS) and inelastic neutron scattering (INS), and iii) first-principles simulations leveraging large-scale computing to identify the fundamental origins of the observed effects, by relating atomic structure and dynamics to electronic orbital interactions. Finally, we modeled and verified the impact of the phonon behavior on thermal transport to identify new strategies for a-priori design of thermal conductivity. Our integrated collaborative approach helped to systematically unravel the effects of anisotropy and bonding anharmonicity on phonon transport, thermodynamics, and thermal properties of complex anisotropic materials.
36 MATERIALS SCIENCE↗
Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane
The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as “membrane-distal” and estimate to comprise ~90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.
KRAS↗
SmartFuse: Reconfigurable Smart Switches to Accelerate Fused Collectives in HPC Applications
Communication switches have sometimes been augmented to process collectives (e.g., the IBM BlueGene project and the Mellanox SHArP switch). In this work, we find that there is a great acceleration opportunity through the further augmentation of switches to accelerate more complex functions that combine communication with computation. We consider three types of such functions. The first is fully-fused collectives built by fusing multiple existing collectives like Allreduce with Alltoall. The second is semi-fused collectives built by combining a collective with another computation. The third we refer to as higher-order collectives built by combining multiple computations and communications, such as to perform matrix-matrix multiply (PGEMM). In this work, we propose a framework called SmartFuse to accelerate fused collective functions. The core of SmartFuse is a reconfigurable smart switch to support these operations. The semi/fully fused collectives are implemented with a CGRAlike architecture, while higher-order collectives are implemented with a more specialized computational unit that can also schedule communication. Supporting our framework is software to evaluate and translate relevant parts of the input program, compile them into a control data flow graph, and then map this graph to the switch hardware. The proposed framework, once deployed, has the strong potential to accelerate existing HPC applications transparently by encapsulation within an MPI implementation. Experimental results show that this approach improves the performance of the PGEMM kernel, MINIFE, and AMG by, on average, 94%, 15%, and 13%, respectively.
Haghi, Pouya↗
C-terminal conformational changes in SCF-D3/MAX2 ubiquitin ligase are required for KAI2-mediated signaling
Karrikins (KARs) are bioactive molecules derived from burning vegetation. Plants perceive KARs through the hydrolase KARRIKIN INSENSITIVE 2 (KAI2) that interacts with the F-box protein ubiquitin ligase MORE AXILLARY GROWTH 2 (MAX2). MAX2 also plays a role in the perception and signal activation by Strigolactone (SL), a phytohormone controlling various developmental processes in plants. SL also acts as a rhizosphere signal to activate arbuscular mycorrhiza fungi that can be exploited by parasitic plants. kai2 knockouts exhibit distinct developmental defects and therefore KAI2 is hypothesized to perceive an unidentified endogenous ligand provisionally termed KAI2-Ligand (KL). Upon KAR/KL perception, the protein complex of KAI2-MAX2 targets SUPPRESSOR OF MAX2-1/2 (SMAX1)/SMXL2 for proteasomal degradation. Despite the identification of the key components KAI2, MAX2, and SMAX1 in KAR/KL signaling, their mode of interaction and regulation remains elusive. Recently, the regulatory function of the conformational switch of MAX2 C-terminal helix (CTH) in SL signaling has been demonstrated however its role in KAR/KL signaling remained unknown. Here we address the function of MAX2-CTH dynamics both in vitro and in planta and show that the central role of CTH is conserved between SL and KAR/KL signaling pathway.
59 BASIC BIOLOGICAL SCIENCES↗
Reversible Switch in Charge Storage Enabled by Selective Ion Transport in Solid Electrolyte Interphase
Solid-electrolyte interphases (SEIs) in advanced rechargeable batteries ensure reversible electrode reactions at extreme potentials beyond the thermodynamic stability limits of electrolytes by insulating electrons while allowing working ions to transport. Such selective ion transport occurs naturally in biological cell membranes as a ubiquitous prerequisite of many life processes and a foundation of biodiversity. In addition, cell membranes can selectively open and close the ion channels in response to external stimuli (e.g., electrical, chemical, mechanical, thermal), giving rise to “gating” mechanisms that help manage intracellular reactions. We wondered whether the chemistry and structure of SEIs can mimic cell membranes, such that ion gating can be replicated. That is, can SEIs realize a reversible switching between two electrochemical behaviors, i.e., the ion intercalation chemistry of batteries and the ion adsorption of capacitors? Herein, we report such SEIs that result in thermally activated selective ion transport. The function of open/close gate switches is governed by the chemical and structural dynamics of SEIs under different thermal conditions, with precise behaviors as conducting and insulating interphases that enable battery and capacitive processes within a finite temperature window. Such an ion gating function is synergistically contributed by Arrhenius-activated ion transport and SEI dissolution/regrowth. Following the understanding of this new mechanism, we then develop an electrochemical method to heal the SEI layer in situ. As a result, the knowledge acquired in this work reveals the possibility of hitherto unknown biomimetic properties of SEIs, which will guide us to leverage such complexities to design better SEIs for future battery chemistries.
25 ENERGY STORAGE↗
Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis
The uridyl transferases TUT4 and TUT7 (collectively called TUT4(7)) switch between two modes of activity, either promoting expression of let-7 microRNA (monoU) or marking it for degradation (oligoU). Lin28 modulates the switch via recruitment of TUT4(7) to the precursor pre-let-7 in stem cells and human cancers. We found that TUT4(7) utilize two multidomain functional modules during the switch from monoU to oligoU. The catalytic module (CM) is essential for both activities, while the Lin28-interacting module (LIM) is indispensable for oligoU. A TUT7 CM structure trapped in the monoU activity staterevealed a duplex-RNA-binding pocket that orients group II pre-let-7 hairpins to favor monoU addition. Conversely, the switch to oligoU requires the ZK domain of Lin28 to drive the formation of a stable ternary complex between pre-let-7 and the inactive LIM. Finally, ZK2 of TUT4(7) aids oligoU addition by engaging the growing oligoU tail through uracil-specific interactions.
59 BASIC BIOLOGICAL SCIENCES↗
Mitogen-activated protein kinase 6 negatively regulates secondary wall biosynthesis by modulating MYB46 protein stability in Arabidopsis thaliana
The R2R3-MYB transcription factor MYB46 functions as a master switch for secondary cell wall biosynthesis, ensuring the exquisite expression of the secondary wall biosynthetic genes in the tissues where secondary walls are critical for growth and development. At the same time, suppression of its function is needed when/where formation of secondary walls is not desirable. Little is known about how this opposing control of secondary cell wall formation is achieved. We used both transient and transgenic expression of MYB46 and mitogen-activated protein kinase 6 (MPK6) to investigate the molecular mechanism of the post-translational regulation of MYB46. We show that MYB46 is phosphorylated by MPK6, leading to site specific phosphorylation-dependent degradation of MYB46 by the ubiquitin-mediated proteasome pathway. In addition, the MPK6-mediated MYB46 phosphorylation was found to regulate in planta secondary wall forming function of MYB46. Furthermore, we provide experimental evidences that MYB83, a paralog of MYB46, is not regulated by MPK6. The coupling of MPK signaling to MYB46 function provides insights into the tissue- and/or condition-specific activity of MYB46 for secondary wall biosynthesis.
59 BASIC BIOLOGICAL SCIENCES↗
PD-L1 induces macrophage polarization toward the M2 phenotype via Erk/Akt/mTOR
Highlights: • PD-L1 treatment upregulates CD206 but not CD86 expression. • PD-L1-induced DEGs are related to the immune response, mitochondrial function, and metabolism. • Nivolumab, LY294002, U0126, and rapamycin inhibit the PD-L1-stimulated CD206 expression. • PD-L1 promotes M2 polarization via Erk/Akt/mTOR. PD-L1 (programmed death-ligand 1) is the ligand of PD-1 (programmed cell death protein 1) and regulates inhibitory immune responses. It is well known that PD-L1 suppresses T cell function via binding to PD-1. However, little is known about the role of the PD-1/PD-L1 axis in macrophage polarization. According to previous studies, the function of the PD-1/PD-L1 axis in macrophage polarization is controversial, and the underlying mechanism has not been fully elucidated. Thus, we treated THP-1-derived macrophages with human PD-L1 Fc to determine the role of the PD-1/PD-L1 axis in macrophage polarization. To further explore the mechanism, we performed RNA sequencing and used specific inhibitors to identify the implicated signalling pathways. In this study, we found that PD-L1 induces the upregulation of CD206 expression, which is inhibited by nivolumab, LY294002, U0126, and rapamycin. Evaluation of differentially expressed genes (DEGs) and bioinformatics analysis indicated that PD-L1 also induces the upregulation of the expression of genes that maintain mitochondrial function and mediate metabolic switching. In addition, we did not detect PD-L1-induced CD86 alterations, indicating that PD-L1 treatment has no significant influence on M1 polarization. Taken together, these results suggest that PD-L1 binds to PD-1 and promotes M2 polarization accompanied by mitochondrial function enhancement and metabolic reprogramming via Erk/Akt/mTOR. This study elucidates the role of PD-L1 in macrophage polarization and verifies the underlying mechanisms for the first time. Considering that aberrantly upregulated PD-L1 expression contributes to a wide variety of diseases, targeting PD-L1-mediated macrophage polarization is a prospective therapeutic strategy for both neoplastic and nonneoplastic diseases.
60 APPLIED LIFE SCIENCES↗
The Influence of Processing Parameters on the Transition Zone for Blended Material 3D Printing
The use of Multiple Materials (MM) in Additive Manufacturing (AM) is increasingly important for expanding the range of applications in the manufacturing industry, particularly for large-format processes. Typically, polymer-based AM incorporates MM transitions through discrete interfaces between layers. This arrangement significantly increases the occurrence of layer delamination failures due to decreased bonding between dissimilar polymers. Elimination of discrete material interfaces by continuously transitioning from Material A to B provides a possible solution. Such continuous gradients could be used to create functionally graded structures that take full advantage of AM’s capability to deliberately impart site-specific properties. Cincinnati’s Big Area Additive Manufacturing (BAAM) system at Oak Ridge National Lab has been equipped with a dual-hopper system that enables in-situ material switching specifically intended for functionally graded and MM printing. The resulting material transition exhibits varied behavior based on printing conditions, which can have an impact on part design and resulting mechanical properties. In this work, the transition zone is characterized as a function of the printing screw speed (related to volumetric flow) and the screw geometry.
Brackett, James↗
Photostability of Ambient-Processed, Conjugated Polymer Electrochromic Devices Encapsulated by Bioderived Barrier Films
Polymer-based electrochromic devices (ECDs) are a promising technology for enabling low-voltage, disposable displays, yet are currently limited by photo-oxidative bleaching of the active materials. Here, renewable barrier films composed of cellulose and chitin are presented as an alternative to poly(ethylene terephthalate) (PET) for encapsulating ECDs. To assess barrier film effectiveness, lateral ECDs composed of poly(3,4-propylenedioxythiophene-(CH 2 OEtHx) 2 ) (P(ProDOT)) active layers were constructed and encapsulated with a multilayer barrier consisting of chitin nanofibers and cellulose nanocrystals spray cast onto a cellulose acetate substrate (oxygen transmission rate (OTR) = 29 cm 3 m –2 day –1 ), a commercially available PET film (OTR = 8.5 cm 3 m –2 day –1 ), and a high-performance PET-Al 2 O 3 multilayer barrier film (OTR < 1 cm 3 m –2 day –1 ). The photodegradation of the P(ProDOT) active layer was determined by measuring the evolution of the colorimetric contrast (ΔE*) and switching speeds as a function of light exposure (100 mW cm –2 , AM 1.5 G light). Photodegradation was found to proceed at a similar rate for all encapsulated devices (roughly 10 times more slowly than unencapsulated devices), highlighting the opportunity for replacing petroleum packaging with bioderived barrier films. Analysis of the switching kinetics, the shifts in optical absorbance, and evidence of chemical degradation indicate that both photochemical breakdown of the electrolyte and cross-linking of the P(ProDOT) active material are key drivers for loss of device performance when oxygen flux to the active material is limited. Furthermore, pathways toward better understanding photodegradation are then proposed with sustainability in mind for future ECD design.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Operation and Control of Soft Switching Solid State Transformer as a Virtual Synchronous Machine for Photovoltaic Application
Possibility for control and operation of a three-phase solid state soft switching transformer based as a virtual synchronous machine or synchronverter has been investigated in this paper. The soft switching solid state transformer is used as an interface between the ac grid and a photovoltaic power generation unit supported by a battery bank. The control architecture investigated in this paper is that of a synchronverter to achieve inertial support to the grid and local loads. The operation of the soft switching solid state transformer has also been investigated as a V S M during unbalanced/distorted grid voltage condition. Control objective to achieve oscillation free power transfer between the ports (photovoltaic, battery and grid) has been achieved. The presented architecture has been verified for several important case studies via numerical simulations based on MATLAB/Simulink domain.
grid current controller↗
A unified mechanism for plant polyketide biosynthesis derived from in silico modeling
Highlights: • A unitary mechanism for the cyclization of tetraketides in stilbene and chalcone synthase. • The identification of an active water that functions as a “Claisen switch” in chalcone synthase. • QM-MM and FMO analysis of model tetraketide ligands highlighting common and disparate components of binding pockets and cyclization sites in stilbene and chalcone synthase. The polyketide synthases found in a variety of plants and fungi provide a varied source of biologically active compounds of pharmacological and medicinal interest. Stilbene synthase and chalcone synthase catalyze the formation of a common tetraketide intermediate, but use different cyclization mechanisms to produce distinct and separate natural products. While key structural differences have been identified to explain this functional diversity, a fuller explication of the factors responsible for this mechanistic disparity is required. Based on the energetics of our models of the bound tetraketides, and our structural analysis of the active sites we propose that a key tautomeric conversion provides a mechanistic framework common to both cyclizations. A previously unidentified active water molecule facilitates cyclization in chalcone synthase through a Claisen mechanism. Such a “Claisen switch” is comparable to the previously characterized “aldol switch” mechanism proposed for the biosynthesis of resveratrol in stilbene synthase.
60 APPLIED LIFE SCIENCES↗
S-Nitrosylation inhibits the kinase activity of tomato phosphoinositide-dependent kinase 1 (PDK1)
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Giant Doping Response of Magnetic Anisotropy in MnTe
Developing simple ways to control spin states in spintronic devices is a crucial step towards increasing their functionality. MnTe is a room-temperature antiferromagnet with promising spintronic properties, including for thermospintronics and magnon-based devices. Here, we show that, in MnTe, less than 1% Li is sufficient to produce a dramatic spin reorientation as observed by neutron diffraction. The behavior of the 0001 magnetic Bragg peak reveals a significant reorientation of the Mn spins from planar in the pure material to almost completely axial with minimal Li doping. Temperature dependence of the magnetic peaks in Li-doped samples indicates that axial spins shift back to planar suddenly upon approaching the Néel temperature (T N = 307 K). Density functional theory calculations support the idea that a shift in the Fermi level caused by doping is responsible for switching the material between two competing magnetic ground states. These results pave the way for developing easy switching of magnetic states in functional materials such as spintronic devices and topological insulators.
36 MATERIALS SCIENCE↗
Thin-Film Thermal Conductivity Measurements Using Superconducting Nanowires
We present a simple experimental scheme for estimating the cryogenic thermal transport properties of thin films using superconducting nanowires. In a parallel array of nanowires, the heat from one nanowire in the normal state changes the local temperature around adjacent nanowires, reducing their switching current. Calibration of this change in switching current as a function of bath temperature provides an estimate of the temperature as a function of displacement from the heater. This provides a method of determining the contribution of substrate heat transport to the cooling time of superconducting nanowire single-photon detectors. Understanding this process is necessary for successful electrothermal modeling of superconducting nanowire systems.
77 NANOSCIENCE AND NANOTECHNOLOGY↗