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At least 667 records · Page 37

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Smart Ventilation Controls for Occupancy and Auxiliary Fan Use Across U.S. Climates

Smart Ventilation has been developed as a way to reduce the energy associated with ventilation by changing when ventilation happens and how much ventilation occurs at any given time. In high performance buildings with low envelope and appliance related loads, ventilation is becoming a bigger part of the total building energy use and needs to be addressed if performance targets are to be met. This work explores the development and performance of smart ventilation controls based on occupancy and auxiliary fan operation that provide annual dwelling unit ventilation equivalence to ASHRAE Standard 62.2-2016. A prototype high performance home compliant with U.S. DOE Building America Zero Energy Ready program requirements was simulated using the REGCAP tool with and without smart controls across 15 U.S. DOE climate zones. Balanced and unbalanced IAQ fans were independently simulated, and all smart controlled fans had airflows double the reference 62.2-2016 airflow. Three idealized occupancy patterns were examined: 1st shift (a typical daily work/school absence), an extended 1st shift with more time spent out of the home evenings and weekends and 3rd shift (night work). The Occupancy controller turns the IAQ fan off during unoccupied periods, and it resumes ventilation upon their return. While unoccupied, contaminants are allowed to accumulate in the space, because occupants are not exposed to these contaminants. When occupants return home, they are exposed to these higher contaminant concentrations, and the controller increases the ventilation rate sufficiently to ensure equivalence with a continuous IAQ fan. Accounting for pollutant emissions that occur during unoccupied periods (as required by ASHRAE 62.2-2016), sharply distinguishes our occupancy controls from past Demand Controlled Ventilation systems. This new accounting method results in equivalent contaminant exposure, as well as lower reductions in average ventilation rates and lower energy savings. Smart controls were demonstrated that saved HVAC energy (i.e., avoided heating/cooling load, as well as fan energy)—averaging between 6 and 46% of ventilation-related energy use depending on the control strategy and occupancy pattern assumptions. The greatest savings were in the combined Auxiliary Fan + Occupancy control. Energy savings increased with climate heating demand and longer unoccupied time periods. The 3rd shift occupancy pattern had better performance, due to the thermal benefit of reducing the ventilation rate during the cold nighttime hours. This same effect provided a cooling energy benefit in hotter locations for the 1st shift. Overall, savings from occupancy-based smart controls were low, because of the recovery period required after occupants return home, during which the airflow is double the 62.2 reference. This recovery is required to maintain equivalence with the ASHRAE standard. Occupancy-based control performance was improved when combined with sensing auxiliary fans and when providing a pre-occupancy flush out of one- or two-hours. Performance was similarly improved if the ASHRAE Standard were to recognize that pollutant emissions are lower during unoccupied periods, iii allowing a lower target ventilation rate during unoccupied periods (not currently in the standard) (see Full vs. Half AEQ in this report). Finally, over-sized unbalanced fans that are cycled on-and-off by a smart controller (or timer) were found to substantially increase annual average air exchange and energy use relative to a continuous unbalanced fan due to the effects of superposition with natural infiltration.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Ultra-sensitive radon assay using an electrostatic chamber in a recirculating system

Rare event searches such as neutrinoless double beta decay and Weakly Interacting Massive Particle detection require ultra-low background detectors. Radon contamination is a significant challenge for these experiments, which employ highly sensitive radon assay techniques to identify and select low-emission materials. This work presents the development of ultra-sensitive electrostatic chamber (ESC) instruments designed to measure radon emanation in a recirculating gas loop, for future lower background experiments. Unlike traditional methods that separate emanation and detection steps, this system allows continuous radon transport and detection. This is made possible with a custom-built recirculation pump. A Python-based analysis framework, PyDAn, was developed to process and fit time-dependent radon decay data. Radon emanation rates are given for various materials measured with this instrument. A radon source of known activity provides an absolute calibration, enabling statistically-limited minimal detectable activities of 20 µBq. These devices are powerful tools for screening materials in the development of low-background particle physics experiments.

47 OTHER INSTRUMENTATION↗

Carbon Removal Accounting for a Sustainable Future: Distributing CO 2 Flows in Multiservice Systems

Carbon dioxide removal (CDR) systems are an integral part of sustainable pathways limiting global warming to less than 2.0 °C. When the sole purpose of CDR is capturing and storing atmospheric CO 2 , carbon registries offer detailed procedures to calculate the carbon removal credits. However, the registries do not address how to distribute CO 2 flows when CDR provides additional services. Standardized, transparent rules for distributing CO 2 flows among CDR services are required for the formation of efficient private and public carbon markets. The lack of such rules could result in double counting if those reductions are allocated to more than one service, decreasing the trustworthiness of carbon removal credits or deterring the delivery of an additional low-carbon service, thus limiting the economic viability and deployment of CDR. We examine allocation rules in carbon registries and carbon accounting guidelines, including their life cycle assessment (LCA) principles. We evaluate physical (mass-based) and non-physical (economic) allocation methods using a generic CDR system and find both to be unworkable. We then develop a mass balance (MB) approach which can reliably allocate captured and stored carbon (CSC) between carbon removal credits and other services based on the value CO 2 removal in those markets. This practical approach to allocation can be used in a transparent way to provide flexibility that would allow CDR services to capture the value of the multiple services they provide and, through this, promote the deployment of these sustainable alternatives.

54 ENVIRONMENTAL SCIENCES↗

Ultra-sensitive radon assay using an electrostatic chamber in a recirculating system

Rare event searches such as neutrinoless double beta decay and Weakly Interacting Massive Particle detection require ultra-low background detectors. Radon contamination is a significant challenge for these experiments, which employ highly sensitive radon assay techniques to identify and select low-emission materials. This work presents the development of ultra-sensitive electrostatic chamber (ESC) instruments designed to measure radon emanation in a recirculating gas loop, for future lower background experiments. Unlike traditional methods that separate emanation and detection steps, this system allows continuous radon transport and detection. This is made possible with a custom-built recirculation pump. A Python-based analysis framework, PyDAn, was developed to process and fit time-dependent radon decay data. Radon emanation rates are given for various materials measured with this instrument. A radon source of known activity provides an absolute calibration, enabling statistically-limited minimal detectable activities of 20 uBq. These devices are powerful tools for screening materials in the development of low-background particle physics experiments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

OzMALDI: A Gas-Phase, In-Source Ozonolysis Reaction for Efficient Double-Bond Assignment in Mass Spectrometry Imaging with Matrix-Assisted Laser Desorption/Ionization

Lipids make up an important class of biomolecules with diverse structures and varied chemical functions. This diversity is a major challenge in chemical analysis and limits our understanding of biological functions and regulation. A major way lipid isomers differ is by double-bond (db) position, and analyzing db-isomers is especially challenging for mass spectrometry imaging (MSI). Ozonolysis can be used to determine the dbposition and has been paired with MSI before. However, previous techniques require increased analysis time to allow for gas-phase reactions within an ion trap or ion mobility cell or additional sample preparation time to allow for offline ozonation. Here, we introduce a new ozonolysis method inside the matrix-assisted laser desorption-ionization (MALDI) source, termed OzMALDI, that simultaneously produces ozonides from all unsaturated lipids. This allows us to determine db-positions without adding additional reaction time while maintaining the high mass resolution provided by Orbitrap MS. This new technique is especially effective at determining multiple db-positions in lipids containing polyunsaturated fatty acids, which is a limitation of many previous techniques. OzMALDI-MSI was applied to the analysis of rat brain and genetically engineered Camelina and soybean seed samples, demonstrating the utility of this method and uncovering novel biological information.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sublimation Kinetics for Individual Graphite and Graphene Nanoparticles (NPs): NP-to-NP Variations and Evolving Structure-Kinetics and Structure-Emissivity Relationships

A single nanoparticle (NP) mass spectrometry method was used to measure sublimation rates as a function of nanoparticle temperature (T NP ) for sets of individual graphite and graphene NPs. Initially, the NP sublimation rates were ~400 times faster than that for bulk graphite, and there were large NP-to-NP variations. Over time, the rates slowed substantially, though remaining well above the bulk rate. The initial activation energies (E a values) were correspondingly low and doubled as a few monolayer’s worth of material were sublimed from the surfaces. The high initial rates and low E a values are attributed to large numbers of edge, defect, and other low coordination sites on the NP surfaces, and the changes are attributed to atomic-scale “smoothing” of the surface by preferential sublimation of the less stable sites. The emissivity of the NPs also changed after heating, most frequently increasing. Here, the emissivity and sublimation rates were anti-correlated, leading to the conclusion that high densities of low-coordination sites on the NP surfaces enhances sublimation but suppresses emissivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

In situ nanoscale imaging of moiré superlattices in twisted van der Waals heterostructures

Abstract Direct visualization of nanometer-scale properties of moiré superlattices in van der Waals heterostructure devices is a critically needed diagnostic tool for study of the electronic and optical phenomena induced by the periodic variation of atomic structure in these complex systems. Conventional imaging methods are destructive and insensitive to the buried device geometries, preventing practical inspection. Here we report a versatile scanning probe microscopy employing infrared light for imaging moiré superlattices of twisted bilayers graphene encapsulated by hexagonal boron nitride. We map the pattern using the scattering dynamics of phonon polaritons launched in hexagonal boron nitride capping layers via its interaction with the buried moiré superlattices. We explore the origin of the double-line features imaged and show the mechanism of the underlying effective phase change of the phonon polariton reflectance at domain walls. The nano-imaging tool developed provides a non-destructive analytical approach to elucidate the complex physics of moiré engineered heterostructures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Thin Triples Expand the Affordable High-Performance Window Options For Retrofit

Sales of high-performance triple-pane windows make up only a small fraction (~3%) of total window sales in the United States with relatively stagnant market growth over the past 20 years. High costs have been the most commonly cited barrier to adoption. The emergence of thin triples that can fit into the glazing pocket of existing double pane windows has the potential to revolutionize the high-performance window market in particular the retrofit market by enabling glass only upgrades for situations where the frames are still in good condition. The retrofit market has other unique challenges not found in new construction that can be solved or reduced by thin triple pane windows. Insert replacements are often pursued instead of full frame replacement, in retrofits, this method reduces the net free area of a window and can turn an egress window into one that no longer meets the net free area requirements for egress. Thin frames minimize such occurrences. However, these thin frames can often not accommodate the weight of a traditional triple pane, thin triples can bring high performance to this situation. Thicker frames can also increase retrofit labor costs because the interior drywall and/or trim molding needs to be cut back to accommodate a thicker frame while thin triples can fit into frames that match the thickness of the existing window. This paper presents information about field test experiences the highlight these retrofit advantages from experiencing the challenges associated with retrofitting a thick frame as well as the supply chain, purchasability, material and labor costs, and real-world energy and non-energy performance associated with the IGU only replacement method.

window retrofits, thin triple-pane windows, high p↗

Models of SIV rebound after treatment interruption that involve multiple reactivation events

In order to assess the efficacy of novel HIV-1 treatments leading to a functional cure, the time to viral rebound is frequently used as a surrogate endpoint. The longer the time to viral rebound, the more efficacious the therapy. In support of such an approach, mathematical models serve as a connection between the size of the latent reservoir and the time to HIV-1 rebound after treatment interruption. The simplest of such models assumes that a single successful latent cell reactivation event leads to observable viremia after a period of exponential viral growth. Here we consider a generalization developed by Pinkevych et al. and Hill et al. of this simple model in which multiple reactivation events can occur, each contributing to the exponential growth of the viral load. We formalize and improve the previous derivation of the dynamics predicted by this model, and use the model to estimate relevant biological parameters from SIV rebound data. We confirm a previously described effect of very early antiretroviral therapy (ART) initiation on the rate of recrudescence and the viral load growth rate after treatment interruption. We find that every day ART initiation is delayed results in a 39% increase in the recrudescence rate (95% credible interval: [18%, 62%]), and a 11% decrease of the viral growth rate (95% credible interval: [4%, 20%]). We show that when viral rebound occurs early relative to the viral load doubling time, a model with multiple successful reactivation events fits the data better than a model with only a single successful reactivation event.

59 BASIC BIOLOGICAL SCIENCES↗

Liquid-phase turbulence measurements in air-water two-phase flows using particle image velocimetry

Liquid-phase turbulence plays a vital role in determining various gas-liquid two-phase flow parameters, such as void fraction distribution, bubble morphology, bubble-bubble interactions, and interfacial area concentration. In this study, a two-phase flow database including both the gas- and liquid-phases measurements was developed focusing on three bubbly flow conditions in an air-water two-phase flow loop with a vertical one-inch diameter circular pipe test section. A particle image velocimetry (PIV) system integrating an optical phase separation method, i.e., the planar laser-induced fluorescence (PLIF) technique using fluorescent particles and optical filtration, was applied to measure the liquid-phase turbulence information, including the time-averaged velocity, Reynolds stress, and turbulent kinetic energy for the liquid phase. The PIV measurements were taken at three ports along the test section at 14.5, 51.5, and 88.5 pipe inner diameters downstream of a bubble injector. In addition, a double-sensor conductivity probe was used to measure radial distributions of the local time-averaged void fraction and gas velocity. The measured liquid-phase turbulence was used to benchmark Sato's turbulence model considering the bubble-induced shear stress for the three tested bubbly flows. The benchmark results showed good agreement between the PIV measurements and model predictions. Lastly, in the two bubbly flows tested that have low void fractions being less than 3%, the effect of the bubble-induced turbulence was found not significant. However, the bubble-induced shear stress becomes important with the increase of the void fraction.

42 ENGINEERING↗

A microfluidic platform for the synthesis of polymer and polymer-protein-based protocells

In this study, we demonstrate the fabrication of polymersomes, protein-blended polymersomes, and polymeric microcapsules using droplet microfluidics. Polymersomes with uniform, single bilayers and controlled diameters are assembled from water-in-oil-in-water double-emulsion droplets. This technique relies on adjusting the interfacial energies of the droplet to completely separate the polymer-stabilized inner core from the oil shell. Protein-blended polymersomes are prepared by dissolving protein in the inner and outer phases of polymer-stabilized droplets. Cell-sized polymeric microcapsules are assembled by size reduction in the inner core through osmosis followed by evaporation of the middle phase. All methods are developed and validated using the same glass-capillary microfluidic apparatus. This integrative approach not only demonstrates the versatility of our setup, but also holds significant promise for standardizing and customizing the production of polymer-based artificial cells.

36 MATERIALS SCIENCE↗

Mercury Speciation of Hanford 241-AP-107 Tank Waste Samples - 20384

The concentration of key mercury species in the Hanford tank waste has not been previously measured. Based on process knowledge, an estimated inventory of 2,100 kg of mercury is assumed and was distributed in varied amounts across 149 single-shell tanks (SSTs) and 28 double-shell tanks (DSTs). Limited analyses of individual SSTs and DSTs for total mercury were all below detection, yielding upper limits in concentration estimates based solely on instrument detection limits, resulting in an uncertain mercury inventory for Hanford tanks. Accurate and reliable chemical speciation and quantification is desired to anticipate, predict, and abate the mass movements of various mercury species through the Hanford waste processing flowsheet. Highly sensitive separation and quantification methods for total, elemental, and monomethyl mercury species, in tank waste, have been developed at the Pacific Northwest National Laboratory's (PNNL) Radiochemical Processing Laboratory (RPL). A non-radiological environmental method to quantify mercury species has been adapted for application to Hanford tank 241-AP-107 raw supernatant feed, filtered feed, and cesium-decontaminated samples. These samples represent feed inventory and pretreatment process effluents prior to immobilization by vitrification. This method separates and preconcentrates total, elemental, and monomethyl mercury onto selective solid substrates with little-to-no radioactive background. The solid samples can then be released from strict radiological control, allowing for analytical work to be conducted in low-level radiological facilities. Separation of mercury species was demonstrated at PNNL's RPL in Richland, Washington before transport and analytical quantification using cold vapor atomic fluorescence spectrometry (CVAFS) at PNNL's Marine Science Laboratory (MSL) in Sequim, Washington. Additional studies were conducted to assess the stability of monomethyl mercury in distilled matrices and preconcentrated onto the Carbotrap{sup R} solid substrate to assess sample degradation over time during transport. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Ab Initio Uncertainty Quantification of Neutrinoless Double-Beta Decay in 76 Ge

The observation of neutrinoless double-beta (0⁢𝜈⁢𝛽⁢𝛽) decay would offer proof of lepton number violation, demonstrating that neutrinos are Majorana particles, while also helping us understand why there is more matter than antimatter in the Universe. If the decay is driven by the exchange of the three known light neutrinos, a discovery would, in addition, link the observed decay rate to the neutrino mass scale through a theoretical quantity known as the nuclear matrix element (NME). Accurate values of the NMEs for all nuclei considered for use in 0⁢𝜈⁢𝛽⁢𝛽 experiments are therefore crucial for designing and interpreting those experiments. Here, we report the first comprehensive ab initio uncertainty quantification of the 0⁢𝜈⁢𝛽⁢𝛽-decay NME, in the key nucleus 76 Ge. Here, our method employs nuclear strong and weak interactions derived within chiral effective field theory and recently developed many-body emulators. Our result, with a conservative treatment of uncertainty, is an NME of 2.60$^{+1.28}_{−1.36}$, which, together with the best-existing half-life sensitivity and phase-space factor, sets an upper limit for effective neutrino mass of 187$^{+205}_{−62}$ meV. The result is important for designing next generation germanium detectors aiming to cover the entire inverted hierarchy region of neutrino masses.

Ab initio calculations↗

Unveiling the Finite Temperature Physics of Hydrogen Chains via Auxiliary Field Quantum Monte Carlo

The ability to accurately predict the finite temperature properties and phase diagrams of realistic quantum solids is central to uncovering new phases and engineering materials with novel properties ripe for device applications. Nonetheless, there remain comparatively few many-body techniques capable of elucidating the finite temperature physics of solids from first principles. Here, we take a significant step toward developing such a technique by generalizing our previous, exact fully ab initio finite temperature Auxiliary Field Quantum Monte Carlo (FT-AFQMC) method to model periodic solids and employing it to uncover the finite temperature physics of periodic hydrogen chains. Our chains’ unit cells consist of 10 hydrogen atoms modeled in a minimal basis, and we sample 5 k-points from the first Brillouin zone to arrive at a supercell consisting of 50 orbitals and 50 electrons. Based upon our calculations of these chains’ many-body energies, free energies, entropies, heat capacities, double and natural occupancies, and charge and spin correlation functions, we outline their metal–insulator and magnetic ordering as a function of both H–H bond distance and temperature. At low temperatures approaching the ground state, we observe both metal–insulator and ferromagnetic–antiferromagnetic crossovers at bond lengths between 0.5 and 0.75 Å. We then demonstrate how this low-temperature ordering evolves into a metallic phase with decreasing magnetic order at higher temperatures. In order to contextualize our results, we compare the features we observe to those previously seen in one-dimensional, half-filled Hubbard models at finite temperature and in ground state hydrogen chains. Interestingly, we identify signatures of the Pomeranchuk effect in hydrogen chains for the first time and show that spin and charge excitations that typically arise at distinct temperatures in the Hubbard model are indistinguishably coupled in these systems. Beyond qualitatively revealing the many-body phase behavior of hydrogen chains in a numerically exact manner without invoking the phaseless approximation, our efforts shed light on the further theoretical developments that will be required to construct the phase diagrams of the more complex transition metal, lanthanide, and actinide solids of longstanding interest to physicists.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extracting Topological Orders of Generalized Pauli Stabilizer Codes in Two Dimensions

In this paper, we introduce an algorithm for extracting topological data from translation invariant generalized Pauli stabilizer codes in two-dimensional systems, focusing on the analysis of anyon excitations and string operators. The algorithm applies to Z d qudits, including instances where d is a nonprime number. This capability allows the identification of topological orders that differ from the Z d toric codes. It extends our understanding beyond the established theorem that Pauli stabilizer codes for Z p qudits (with p being a prime) are equivalent to finite copies of Z p toric codes and trivial stabilizers. The algorithm is designed to determine all anyons and their string operators, enabling the computation of their fusion rules, topological spins, and braiding statistics. The method converts the identification of topological orders into computational tasks, including Gaussian elimination, the Hermite normal form, and the Smith normal form of truncated Laurent polynomials. Furthermore, the algorithm provides a systematic approach for studying quantum error-correcting codes. We apply it to various codes, such as self-dual CSS quantum codes modified from the two-dimensional honeycomb color code and non-CSS quantum codes that contain the double semion topological order or the six-semion topological order. Published by the American Physical Society 2024

Physics↗

Isochronous and period-doubling diagrams for symplectic maps of the plane

Symplectic mappings of the plane serve as key models for exploring the fundamental nature of complex behavior in nonlinear systems. Central to this exploration is the effective visualization of stability regimes, which enables the interpretation of how systems evolve under varying conditions. While the area-preserving quadratic Hénon map has received significant theoretical attention, a comprehensive description of its mixed parameter-space dynamics remain lacking. This limitation arises from early attempts to reduce the full two-dimensional phase space to a one-dimensional projection, a simplification that resulted in the loss of important dynamical features. Consequently, there is a clear need for a more thorough understanding of the underlying qualitative aspects. This paper aims to address this gap by revisiting the foundational concepts of reversibility and associated symmetries, first explored in the early works of G.D. Birkhoff. We extend the original framework proposed by Hénon by adding a period-doubling diagram to his isochronous diagram, which allows to represents the system’s bifurcations and the groups of symmetric periodic orbits that emerge in typical bifurcations of the fixed point. A qualitative and quantitative explanation of the main features of the region of parameters with bounded motion is provided, along with the application of this technique to other symplectic mappings, including cases of multiple reversibility. Modern chaos indicators, such as the Reversibility Error Method (REM) and the Generalized Alignment Index (GALI), are employed to distinguish between various dynamical regimes in the mixed space of variables and parameters. These tools prove effective in differentiating regular and chaotic dynamics, as well as in identifying twistless orbits and their associated bifurcations. Additionally, we discuss the application of these methods to real-world problems, such as visualizing dynamic aperture in accelerator physics, where our findings have direct relevance.

43 PARTICLE ACCELERATORS↗