Structurally distinct external solvent-exposed domains drive replication of major human prions
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99 GENERAL AND MISCELLANEOUS↗
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Block Copolymer-Templated Synthesis of Fe–Ni–Co-Modified Nanoporous Alumina Films
Despite intense interest in the catalytic potential of transition metal oxide heterostructures, originating from their large surface area and tunable chemistry, the fabrication of well-defined multicomponent oxide coatings with controlled architectures remains challenging. Here, we demonstrate a simple and effective swelling-assisted sequential infiltration synthesis (SIS) strategy to fabricate hierarchically porous multicomponent metal-oxide electrocatalysts with tunable bimetallic composition. A combination of solution-based infiltration (SBI) of transition metals, iron (Fe), nickel (Ni), and cobalt (Co), into a block copolymer (PS73-b-P4VP28) template, followed by vapor-phase infiltration of alumina using sequential infiltration synthesis (SIS), was employed to synthesize porous, robust, conformal and transparent multicomponent metal-oxide coatings like Fe/AlO x , Fe+Ni/AlO x , and Fe+Co/AlO x . Electrochemical assessments for the oxygen evolution reaction (OER) in a 0.1 M KOH electrolyte demonstrated that the Fe+Ni/AlO x composite exhibited markedly superior catalytic activity, achieving an impressive onset potential of 1.41 V and a peak current density of 3.29 mA/cm 2 . This superior activity reflects the well-known synergistic effect of alloying transition metals with a trace of Fe, which facilitates OER kinetics. Overall, our approach offers a versatile and scalable path towards the design of stable and efficient catalysts with tunable nanostructures, opening new possibilities for a wide range of electrochemical energy applications.
conformal films↗
Nonlinear Shear Rheology of Entangled Polymer Rings
Steady-state shear viscosity η($\bar{γ}$) of unconcatenated ring polymer melts as a function of the shear rate $\bar{γ}$ is studied by a combination of experiments, simulations, and theory. Experiments using polystyrenes with Z ≈ 5 and Z ≈ 11 entanglements indicate weaker shear thinning for rings compared to linear polymers exhibiting power law scaling of shear viscosity η ~ $\bar{γ}$ –0.56 ± 0.02 , independent of chain length, for Weissenberg numbers up to about 10 2 . Nonequilibrium molecular dynamics simulations using the bead-spring model reveal a similar behavior with η ~ $\bar{γ}$ -0.57 ± 0.08 for 4 ≤ Z ≤ 57. Viscosity decreases with chain length for high $\bar{γ}$. In our experiments, we see the onset of this regime, and in simulations, which we extended to Wi ~ 10 4 , the nonuniversality is fully developed. In addition to a naive scaling theory yielding for the universal regime η ~ $\bar{γ}$ –0.57 , we developed a novel shear slit model explaining many details of observed conformations and dynamics as well as the chain length-dependent behavior of viscosity at large $\bar{γ}$. The signature feature of the model is the presence of two distinct length scales: the size of tension blobs and much larger thickness of a shear slit in which rings are self-consistently confined in the velocity gradient direction and which is dictated by the size of a chain section with relaxation time 1/$\bar{γ}$. These two length scales control the two normal stress differences. In this model, the chain length-dependent onset of nonuniversal behavior is set by tension blobs becoming as small as about one Kuhn segment. This model explains the approximate applicability of the Cox–Merz rule for ring polymers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Assessment the leaching characteristics and long-term leaching behavior of some radionuclides from synthesized zeolite cement matrix
Highlights: • Synthesis and characterization of zeolite cement synthesized from fly ash • Leaching tests were used to assess the release rate of {sup 85}Sr and {sup 60}Co radionuclides. • Simple mathematical models were used to detect leaching mechanisms. • Long-term leaching behavior of {sup 85}Sr and {sup 60}Co from cementitious matrix was assessed. The development of cementitious materials remains a vital goal to produce valuable products with good mechanical, physical and chemical properties suitable for the safe disposal of concentrated radionuclides resulted from the treatment of contaminated solutions. In this paper, zeolite cement with good properties was laboratory synthesized from industrial by-products fly ash and characterized using various characterization techniques. The leaching characteristics of strontium and cobalt radionuclides from the synthesized zeolite cement were scrutinized conforming with the standard leaching methodology of International Atomic Energy Authority (IAEA). A mechanical strength assessment was executed to characterize the extent of immobilization process of the solidified matrices. The cumulative leaching fraction (φ) of the two studied radionuclides was found to be less than 5% in all examined conditions, which implies the applicability of the IAEA-recommended methodology for estimating the diffusion coefficient. The experimental leaching data were regressed nonlinearly to various mathematical kinetic models to assess the controlling leaching mechanism and to determine the leaching parameters. The regression results indicated that strontium ({sup 85}Sr) and cobalt ({sup 60}Co) leaching resulted from two succeeding mechanisms: as first order kinetic reaction, and then diffusion. The calculated values of leachability indices signify that the performance of each of the studied matrices is within an acceptable range. A simplified mathematical model, rooted in the first order reaction and diffusion mechanisms, was simulated to predict the radionuclides leaching rates from zeolite cement matrices. By comparing the synthesized zeolite cement with other cementitious materials, it can be concluded that the synthesized material can be classified as an efficient material suitable to immobilize {sup 85}Sr and {sup 60}Co from radioactive wastes. The acquired findings demonstrated that the studied immobilized waste matrices have acceptable mechanical effectiveness.
36 MATERIALS SCIENCE↗
Implication of rare genetic variants of NODAL and ACVR1B in congenital heart disease patients from Indian population
Highlights: • Screening of 300 CHD patients revealed two rare missense variants (p.P51L & p.D327E) in NODAL. • A novel missense variation p.M345I was identified in ACVR1B. • Bioinformatic analyses suggested that these variants could have deleterious role. • Three-dimensional modelling suggested conformation changes in the mutated proteins compared to wild-type. • In vitro studies demonstrated that missense variants affect the function of NODAL and ACVR1B. NODAL signaling plays an essential role in vertebrate embryonic patterning and heart development. Accumulating evidences suggest that genetic mutations in TGF-β/NODAL signaling pathway can cause congenital heart disease in humans. To investigate the implication of NODAL signaling in isolated cardiovascular malformation, we have screened 300 non-syndromic CHD cases and 200 controls for NODAL and ACVR1B by Sanger sequencing and identified two rare missense (c.152C > T; p.P51L and c.981 T > A; p.D327E) variants in NODAL and a novel missense variant c.1035G > A; p.M345I in ACVR1B. All these variants are absent in 200 controls. Three-dimensional protein-modelling demonstrates that both p.P51L and p.D327E variations of NODAL and p.M345I mutation of ACVR1B, affect the tertiary structure of respective proteins. Variants of NODAL (p.P51L and p.D327E) and ACVR1B (p.M345I), significantly reduce the transactivation of AR3-Luc, (CAGA){sub 12}-Luc and (SBE){sub 4}-Luc promoters. Moreover, qRT-PCR results have also deciphered a reduction in the expression of cardiac-enriched transcription factors namely Gata4, Nkx2-5, and Tbx5 in both the mutants of NODAL. Decreased expression of, Gata4, Nkx2-5, Tbx5, and lefty is observed in p.M345I mutant of ACVR1B as well. Additionally, reduced phosphorylation of SMAD2/3 in response to these variants, suggests impaired NODAL signaling and possibly responsible for defective cell fate decision and differentiation of cardiomyocytes leading to CHD phenotype.
60 APPLIED LIFE SCIENCES↗
Surface chemistry-mediated modulation of adsorbed albumin folding state specifies nanocarrier clearance by distinct macrophage subsets
Controlling nanocarrier interactions with the immune system requires a thorough understanding of the surface properties that modulate protein adsorption in biological fluids, since the resulting protein corona redefines cellular interactions with nanocarrier surfaces. Albumin is initially one of the dominant proteins to adsorb to nanocarrier surfaces, a process that is considered benign or beneficial by minimizing opsonization or inflammation. Here, we demonstrate the surface chemistry of a model nanocarrier can be engineered to stabilize or denature the three-dimensional conformation of adsorbed albumin, which respectively promotes evasion or non-specific clearance in vivo. Interestingly, certain common chemistries that have long been considered to convey stealth properties denature albumin to promote nanocarrier recognition by macrophage class A1 scavenger receptors, providing a means for their eventual removal from systemic circulation. We establish that the surface chemistry of nanocarriers can be specified to modulate adsorbed albumin structure and thereby tune clearance by macrophage scavenger receptors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Home Energy Professionals Certifications ISO/IEC 17024: 2021 Policies and Procedures Manual
The U.S. Department of Energy (DOE) enlisted its National Renewable Energy Laboratory (NREL) to coordinate the development of a framework for new certifications in the weatherization and home performance industry. The Home Energy Professional certifications support DOE's Weatherization Assistance Program (WAP) and the broader residential home performance industry through the credentialing process of defined job task analysis for energy auditors and quality control inspectors. The HEP certifications are not intended to supplant or infringe upon any existing industry-recognized credentials, however, the WAP and the home performance industry have utilized the advanced HEP certifications to promote quality work and standardized job task analysis since 2010. On an ongoing basis, NREL brings industry practitioners and subject matter experts together to develop, review, and revise the certification schemes in accordance with the International Organization for Standardization (ISO)/International Electrotechnical Commission (IEC) 17024 standard, "Conformity assessment - General requirements for bodies operating certification of persons" (ISO/IEC 17024). This handbook covers the policies and procedures for the process of developing, maintaining, and validating the certification schemes. Each policy and procedure includes the relevant ISO/IEC 17024 section at the beginning.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Scalable Nano-Scaffold SOFC Anode Architecture Enabling Direct Hydrocarbon Utilization
This project is based on WVU’s pending patents, technology and aims to design and modify the internal surfaces of the Ni/YSZ anode from currently commercially viable Solid Oxide Fuel Cells (SOFCs) using the additive manufacturing process of Atomic Layer Deposition (ALD). The surface architecture/scaffold added onto the internal surface of the anode possesses an engineered nanostructure but it features only commonly-used oxide conductors and electro-catalyst materials. The surface layer possesses a minimum thickness of ~2-40 nm and is solely designed to control the surface reforming reactions and to increase catalytic activity. Three-dimensional (3D) nano scaffold architectures with the noble metal nano-catalyst, low-cost bimetallic catalytic alloys, and nano-scale ionic conducting oxide fully compatible with the state-of-the-art Ni/YSZ anode, were applied to the internal surface of the entire porous SOFC anode using ALD. In the present work, the surface scaffold architecture is essentially multi-functional at the nano-scale, facilitated by the multiple heterostructured interfaces. It will significantly enhance the power density and cell durability for direct hydrocarbon utilization by (1) increasing the number of electrochemical reaction sites to enhance the hydrogen/hydrocarbon oxidation reactions; (2) reducing carbon formation; (3) mitigating the coarsening of backbone Ni phase and the oxidation attack of Ni from oxidants (e.g., H2O, CO2); and (4) promoting the internal reforming capabilities, especially for natural gas applications. ALD is employed to generate stable anode surface architectures that are uniform, precisely controllable at the atomic scale, and accurately repeatable for processing. The engineered anode surface nano-scaffold architecture was cataloged and analyzed using High-resolution Transmission Electron Microscopy (TEM), and cell power/durability performance assessed via comprehensive electrochemical performance testing with commercial specimens and relevant environments using hydrocarbon fuels. To the best of our knowledge, this project is the First Report on ALD of Ni/YSZ. The actual achievement of this Project includes (1). Successful demonstration of 7 types of ALD layers on Ni/YSZ anode, including Co, Ni, Mn, Pt, Ru, ZrOx and multi-functional nano-composite. (1). Conformal coating and subsequently spontaneously pinning the discrete nano-catalyst, including the precious metal nano-catalyst and the Ni and Co catalysts, on the YSZ surface upon the electrochemical operation in the reduced atmosphere. Those nano-catalysts on the ionic-conducting YSZ provided excellent sites for promoting internal reforming; (2). Demonstrated ALD coating increased both catalytic activity and conductivity of Ni/YSZ. Conformal coating provided dopants and introduced additional electrical conducting pathways on the YSZ ionic conductor. The doped surface layer of YSZ with mixed conductivity thus further introduces the active triple phase boundaries adjacent to the ALD-coated nano-catalysts such as Pt, Co, and Ni that are pinned on the YSZ surface. The nano-composite ALD coating on Ni/YSZ anode has significantly increased cell durability; and (3). ALD coating of Ni/YSZ anode increased the power density of the entire cell by 300%. For a long time, the SOFC performance, such as the power density, was deemed hindered by the cathode. The sluggish oxygen reduction reaction (ORR) in the cathode was deemed as hindering the power density of the SOFCs. For the anode-supported commercial SOFCs, the cell performance is considered to be limited by the cathode's performance. For the first time in the field of SOFC, this project has demonstrated that (1). the performance of commercial SOFCs can be further increased by the ALD coating on Ni/YSZ anode backbone. (2). ALD coating on Ni/YSZ fuel electrodes results in the enhancement of power density, and increased reliability, robustness, and endurance of SOFCs, for their application using both hydrogen and hydrocarbon fuels over the entire operating temperature range of 650-800ºC for the inherently functional commercial cells. (3). ALD coating provides alternative approaches of exsolutions for introducing the stable catalyst onto the internal surface of the Ni/YSZ electrode. ALD coating could be much more versatile than exsolution in employing the catalysts with various chemistries onto the various backbones. (4). Due to the negligible amount of ALD materials coated onto the internal surface of the porous cathode of the as-fabricated cells, a peak power density increase up to 300 % induced by ALD coating was simultaneously achieved in terms of both power density and specific power. (5). The ALD coating developed through this project was applied to both the SOFC and Solid Oxide Electrolysis Cells (SOEC). SOEC’s face a similar but more demanding need to improve the fuel electrode's performance. It opens further research directions for electrocatalytic surface nanoionics with a wide range of chemistry. It will revolutionize our ability to render the formation of a nanostructured electrode that has been constantly pursued yet barely achieved for practical SOFC/SOEC applications. The research is also immediately transformative since both the preliminary data and the proposed work are on the direct implantation of nanoionics into the state-of-the-art inherently functional SOCs. It represents an immediate impact on the commercial sectors in SOC technology since the applied ALD processing is computer-controlled ALD coating using the commercial ALD systems, and it is scalable to both the single cells and SOC stacks.
36 MATERIALS SCIENCE↗
Tuning Epoxy Thermomechanics via Thermal Isomerization: A Route to Negative Coefficient of Thermal Expansion Materials
Fine control over the thermal expansion and contraction behavior of polymer materials is challenging. Most polymers have large coefficients of thermal expansion (CTEs), which preclude long performance lifetimes of composite materials. Herein, we report the design and synthesis of epoxy thermosets with low CTE values below their T g and large contraction behavior above T g by incorporating thermally contractile dibenzocyclooctane (DBCO) motifs within the thermoset network. This atypical thermomechanical behavior was rationalized in terms of a twist-boat to chair conformational equilibrium of the DBCO linkages. We anticipate these findings to be generally useful in the preparation of materials with designed CTE values.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Controlling Nanoscale Pore Size and Wall Composition in Polycarbonate Membranes via Atomic Layer Deposition and Sequential Infiltration Synthesis: Implications for High Water Permeance
Polymer membranes have a wide variety of applications, ranging from water treatment to energy storage. Many of these applications require precise control over the membrane porosity and surface chemistry. In this study, we explore the modification of isoporous polycarbonate (PC) track-etched membranes (PCTEs) by atomic layer deposition (ALD) and sequential infiltration synthesis (SIS) to tune the pore size and the pore wall surface chemistry. We first performed a detailed study of Al 2 O 3 ALD and SIS in PCTE using a variety of in situ and ex situ measurements. We discovered that short precursor exposure times are critical to achieve conformal Al 2 O 3 ALD in the PCTE nanopores, while longer precursor exposure times resulted in Al 2 O 3 SIS within the bulk of the PC leaving the membranes brittle. Next, we tuned the PCTE pore size via Al 2 O 3 ALD and studied its effect on the water contact angle and the water permeance. Here, we found that the membranes became more hydrophilic, and the permeance decreased with increasing ALD Al 2 O 3 cycles. Finally, we studied the effect of hydrophilic (SnO 2 )/hydrophobic (In 2 O 3 ) ALD metal oxide coatings on membrane properties. We found that the most hydrophilic SnO 2 showed the highest water flux and the least hydrophilic In 2 O 3 showed the lowest water flux through the PCTE membranes. Our results demonstrate that ALD is an effective method to tune the surface and transport properties of PCTE membranes, but care must be exercised to avoid SIS and bulk modification of the polymer.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks
Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.
Shen, Runze [Univ. of Texas, Houston, TX (United S↗
Comparing simulated demand flexibility against actual performance in commercial office buildings
Commercial building energy benchmarking has been used as a mechanism to evaluate energy use of a single building over time, relative to other similar buildings, or to simulations of a reference building conforming to various energy standards. Lack of empirical demand flexibility data and consistent flexibility metrics has limited the ability to compare demand flexibility performance with estimated demand flexibility in buildings. In this study, we collected demand response performance data for a total of 831 demand response events from 192 sites as a first step to build such a building demand flexibility dataset, and propose a standard core data schema to consolidate field data from different sources. We also performed parametric simulations of a control strategy called “global temperature adjustment” using commercial office prototype building models. We then compared the simulated demand flexibility performance against the actual data for offices with global temperature adjustment strategy implemented. During demand response events with an average outside air temperature of 34 °C (range 23 °C–42 °C), the measured demand decrease intensity of the demand flexibility metrics were 6.1 watts per square meter (W/m 2 ), 10.0 W/m 2 , 11.1 W/m 2 , 7.1 W/m 2 , and 4.7 W/m 2 for small, small–medium, medium, medium–large, and large office buildings, respectively. Compared to the measured data in medium- and large-size buildings, the simulated demand decrease intensity was 0.7 W/m 2 (17%) lower on average. The discrepancy between simulated and measured peak demand intensities fell within one standard deviation of the mean measured data. Here, the comparison results validate the credibility of simulations in capturing real building data for assessing the technical potential of building demand flexibility.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12
Cobalamin is a complex organometallic cofactor that is processed and targeted via a network of chaperones to its dependent enzymes. AdoCbl (5'-deoxyadenosylcobalamin) is synthesized from cob(II)alamin in a reductive adenosylation reaction catalyzed by adenosyltransferase (ATR), which also serves as an escort, delivering AdoCbl to methylmalonyl-CoA mutase (MCM). The mechanism by which ATR signals that its cofactor cargo is ready (AdoCbl) or not [cob(II)alamin] for transfer to MCM, is not known. In this study, we have obtained crystallographic snapshots that reveal ligand-induced ordering of the N terminus of Mycobacterium tuberculosis ATR, which organizes a dynamic cobalamin binding site and exerts exquisite control over coordination geometry, reactivity, and solvent accessibility. Cob(II)alamin binds with its dimethylbenzimidazole tail splayed into a side pocket and its corrin ring buried. The cosubstrate, ATP, enforces a four-coordinate cob(II)alamin geometry, facilitating the unfavorable reduction to cob(I)alamin. The binding mode for AdoCbl is notably different from that of cob(II)alamin, with the dimethylbenzimidazole tail tucked under the corrin ring, displacing the N terminus of ATR, which is disordered. In this solvent-exposed conformation, AdoCbl undergoes facile transfer to MCM. The importance of the tail in cofactor handover from ATR to MCM is revealed by the failure of 5'-deoxyadenosylcobinamide, lacking the tail, to transfer. In the absence of MCM, ATR induces a sacrificial cobalt–carbon bond homolysis reaction in an unusual reversal of the heterolytic chemistry that was deployed to make the same bond. Finally, the data support an important role for the dimethylbenzimidazole tail in moving the cobalamin cofactor between active sites.
59 BASIC BIOLOGICAL SCIENCES↗
Disease phenotype of classical sheep scrapie is changed upon experimental passage through white-tailed deer
Prion agents occur in strains that are encoded by the structure of the misfolded prion protein (PrP Sc ). Prion strains can influence disease phenotype and the potential for interspecies transmission. Little is known about the potential transmission of prions between sheep and deer. Previously, the classical US scrapie isolate (No.13-7) had a 100% attack rate in white-tailed deer after oronasal challenge. The purpose of this study was to test the susceptibility of sheep to challenge with the scrapie agent after passage through white-tailed deer (WTD scrapie). Lambs of various prion protein genotypes were oronasally challenged with WTD scrapie. Sheep were euthanized and necropsied upon development of clinical signs or at the end of the experiment (72 months post-inoculation). Enzyme immunoassay, western blot, and immunohistochemistry demonstrated PrP Sc in 4 of 10 sheep with the fastest incubation occurring in VRQ/VRQ sheep, which contrasts the original No.13-7 inoculum with a faster incubation in ARQ/ARQ sheep. Shorter incubation periods in VRQ/VRQ sheep than ARQ/ARQ sheep after passage through deer was suggestive of a phenotype change, so comparisons were made in ovinized mice and with sheep with known strains of classical sheep scrapie: No. 13–7 and x-124 (that has a more rapid incubation in VRQ/VRQ sheep). After mouse bioassay, the WTD scrapie and x-124 isolates have similar incubation periods and PrP Sc conformational stability that are markedly different than the original No. 13–7 inoculum. Furthermore, brain tissues of sheep with WTD scrapie and x-124 scrapie have similar patterns of immunoreactivity that are distinct from sheep with No. 13–7 scrapie. Multiple lines of evidence suggest a phenotype switch when No. 13–7 scrapie prions are passaged through deer. This represents one example of interspecies transmission of prions resulting in the emergence or selection of new strain properties that could confound disease eradication and control efforts.
59 BASIC BIOLOGICAL SCIENCES↗
Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin
Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.
Amines↗
Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs
Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.
59 BASIC BIOLOGICAL SCIENCES↗
Machine Learning with Gradient-Based Optimization of Nuclear Waste Vitrification with Uncertainties and Constraints
Gekko is an optimization suite in Python that solves optimization problems involving mixed-integer, nonlinear, and differential equations. The purpose of this study is to integrate common Machine Learning (ML) algorithms such as Gaussian Process Regression (GPR), support vector regression (SVR), and artificial neural network (ANN) models into Gekko to solve data based optimization problems. Uncertainty quantification (UQ) is used alongside ML for better decision making. These methods include ensemble methods, model-specific methods, conformal predictions, and the delta method. An optimization problem involving nuclear waste vitrification is presented to demonstrate the benefit of ML in this field. ML models are compared against the current partial quadratic mixture (PQM) model in an optimization problem in Gekko. GPR with conformal uncertainty was chosen as the best substitute model as it had a lower mean squared error of 0.0025 compared to 0.018 and more confidently predicted a higher waste loading of 37.5 wt% compared to 34 wt%. The example problem shows that these tools can be used in similar industry settings where easier use and better performance is needed over classical approaches. Future works with these tools include expanding them with other regression models and UQ methods, and exploration into other optimization problems or dynamic control.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Pressure–Modulated Luminescence Enhancement and Quenching in a Hydrogen–Bonded Organic Framework
Light emission in the solid state is central for illumination, sensing, and imaging applications. Unlike luminescence in dilute solutions, where the excited states are unimolecular in nature, intermolecular interaction plays a significant role in the quantum yield of solid-state luminophores, manifested as competing aggregation-caused quenching (ACQ) and aggregation-induced enhancement (AIE). Both effects are extensively studied in various systems; however, it remains unclear how their competition depends on molecular conformation and intermolecular stacking. Here the direct observation of pressure-modulated AIE-ACQ competition in a crystalline hydrogen-bonded organic framework (HOF) is reported. Using in situ spectroscopies and computational modeling, the intramolecular vibration and intermolecular π–π stacking directly responsible for the non-radiative decay of the excited state are identified. The extent of these two contributions is modulated by hydrostatic pressure and guest molecules in the HOF pores. Furthermore, this work demonstrates a physically neat model system to understand and control solid-state luminescence, and a potential material platform for piezoluminescent sensing.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗