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At least 415 records · Page 23

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗

Diffusion of Hydrophilic to Hydrophobic Forms of Nile Red in Aqueous C 12 EO 10 Gels by Variable Area Fluorescence Correlation Spectroscopy

In this work, solute diffusion within lyotropic liquid crystal gels prepared from a series of water and decaethylene glycol monododecyl ether (C 12 EO 10 ) mixtures was explored by variable area fluorescence correlation spectroscopy. Aqueous C 12 EO 10 gels were prepared in concentrations ranging from 55:45 to 70:30 wt% of surfactant and water. Small angle X-ray scattering revealed that these gels comprise hexagonal mesophases of cylindrical micelles. Micelle spacing was found to decrease with increasing C 12 EO 10 concentration. Three different Nile red (NR) dyes were employed as model solutes and were separately doped into the gels at nanomolar levels. These include a hydrophilic form of NR incorporating an anionic sulfonate group (NRSO 3 - ), a hydrophobic form incorporating a fourteen-carbon alkane tail (NRC 14 ), and commercial NR as an intermediate case. FCS data acquired from the gels revealed that NRSO 3 - diffused primarily in 3D. Its diffusion coefficient exhibited a monotonic decrease with increasing gel concentration and micelle packing density, consistent with confinement of its motions as a result of its exclusion from the micelle cores. NRC 14 exhibited the smallest diffusion coefficient, most likely due to its larger size and enhanced interactions with the micelle cores. NR yielded an intermediate diffusion coefficient and the most anomalous behavior of the three dyes, attributable to its facile partitioning between core and corona regions, and greater participation by 1D diffusion. The results of these studies afford an improved understanding of molecular mass transport through soft-matter nanomaterials like those being developed for use in drug delivery and membrane based chemical separations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermally Insulating Transparent Barrier (THINNER) coatings on single pane windows

Conventional silica aerogel monoliths can provide remarkable thermal insulation but the presence of large pores (> 30 nm) tends to scatter visible light and render the material opaque or translucent instead of transparent. In addition, they are prone to cracking during synthesis and handling which makes them difficult to integrate in products and in particular in window solutions. This project developed two new solgel synthesis methods using silica precursors or preformed silica nanoparticles and ambient drying to produce mesoporous organo-silica monoliths. The monoliths were (i) thermally insulating, (ii) optically transparent, (iii) flexible, and (iv) hydrophobic. They feature porosity ranging from 50% to 90% with narrow pore size distribution with pore less than 20 nm resulting in excellent optical clarity (haze < 2%) and very low thermal conductivity (< 30 mW/mK). Interestingly, not only porosity but also pore size and mass fractal dimension were found to affect the thermal conductivity of the mesoporous silica. The superior transparency of the monoliths was shown to be attributed to dependent scattering among silica nanoparticles. Flexibility was achieved through trimethylchlorosilane surface modification. Furthermore, process scale-up and integration of the ambigel monoliths into window solutions using optically clear adhesives were also demonstrated in 6”x6” double-pane windows. The aerogel and the window solution were shown to be durable to accelerated aging under UV, moisture, and/or temperature gradient and thermal cycling. Overall, the window solution achieved the technical performance and the cost target of $10/sqft set for the SHIELD program. However, scaling to industry relevant scale (> 10’x10’) remains a challenge due to requirements on the drying process and fume hood size and to the propensity of large aerogel slab to crack during drying.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Mesoporous Silica Formation Mechanisms Probed Using Combined Spin–Echo Modulated Small-Angle Neutron Scattering (SEMSANS) and Small-Angle Neutron Scattering (SANS)

In this work, the initial formation stages of surfactant-templated silica thin films which grow at the air–water interface were studied using combined spin–echo modulated small-angle neutron scattering (SEMSANS) and small-angle neutron scattering (SANS). The films are formed from either a cationic surfactant or nonionic surfactant (C 16 EO 8 ) in a dilute acidic solution by the addition of tetramethoxysilane. Previous work has suggested a two stage formation mechanism with mesostructured particle formation in the bulk solution driving film formation at the solution surface. From the SEMSANS data, it is possible to pinpoint accurately the time associated with the formation of large particles in solution that go on to form the film and to show their emergence is concomitant with the appearance of Bragg peaks in the SANS pattern, associated with the two-dimensional hexagonal order. The combination of SANS and SEMSANS allows a complete depiction of the steps of the synthesis that occur in the subphase.

36 MATERIALS SCIENCE↗

Unit-density SU(3) Fermi-Hubbard model with spin-flavor imbalance

The advent of ultracold alkaline-earth atoms in optical lattices has established a platform for investigating correlated quantum matter with SU⁡(𝑁) symmetry, offering highly tunable model parameters that allow experiments to access phenomena that are unavailable in conventional materials. Understanding the ground-state physics of SU⁡(𝑁) Fermi-Hubbard models away from the Heisenberg limit and from the spin-flavor balanced setting is important, as examining the flavor imbalance reveals new physics in Fermi-Hubbard models and shows how SU⁡(𝑁) phases react to practical experimental imperfections in optical lattices. Here, in this study, mean-field phase diagrams are presented for the unit-density SU(3) Fermi-Hubbard model at two sets of flavor densities, ($\frac{1}{3}$ − 𝛿, $\frac{1}{3}$ + 𝛿, $\frac{1}{3}$) and ($\frac{1}{4}$ − 𝛿, $\frac{1}{4}$ +𝛿, $\frac{1}{2}$), with the flavor imbalance introduced as 𝛿. Novel phases are identified at moderate interaction strengths for both densities, and their robustness is investigated in the presence of flavor imbalance. Furthermore, we provide microscopic explanations of the phases found and their stability. Analysis of thermal ensembles of random mean-field solutions indicate that, at temperatures accessible in state-of-the-art cold atom experiments, some spin orders are hard for conventional scattering or local observable measurements to detect, but can be more accessible with quantum gas microscopy in optical lattice experiments. This work also shows that nesting and Mottness, intertwined in the usual SU(2) Hubbard model in stark contrast to generic materials, can be tuned in the SU(3) model and play distinct roles. The resulting phase diagrams not only deepen our understanding of SU⁡(𝑁) Fermi-Hubbard models but also inform future experimental search for new phases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Exact evaluation of large-charge correlation functions in nonrelativistic conformal field theory

The large-charge master field which generates all n -point correlation functions with an insertion of large charge Q in nonrelativistic conformal field theory is obtained. This field is used to compute Schrödinger-invariant n -point correlation functions of large-charge operators via a direct evaluation of the path integral. Conformal dimensions are found to agree with calculations based on the state-operator correspondence. The master field solution exhibits an emergent harmonic trap whose frequency is a function of the Euclidean time. The large-charge effective action with operator insertions describes a droplet of superfluid matter whose spatial size scales with the time separation of sources. The solution is used to compute Schrödinger symmetry breaking corrections in the large-charge effective field theory (EFT) due to a finite scattering length in the fundamental theory of fermions near unitarity. The scaling of these effects in the large-charge power counting scheme is established, and the size of the effects is quantified using input from quantum Monte Carlo simulations of the near-unitary gas, as well as from the large- N expansion at large charge. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Applicability of 1D site response analysis to shallow sedimentary basins: A critical evaluation through physics-based 3D ground motion simulations

One-dimensional site response analysis (1D SRA) remains the standard practice in considering the effect of local soil deposits and predicting site-specific ground motions, although its range of applicability to realistic seismic wavefields is still in question. In this 1D approach, horizontal and vertical ground shaking are assumed to be induced by vertically propagating shear and compressional waves, respectively. A recent study based on analytical two-dimensional (2D) plane waves and simple point source earthquake simulations has shown two mechanistic limitations in this 1D modelling technique for general inclined seismic waves, that is, systematic over-prediction of the vertical motion and wave trapping in the 1D soil column. In this article, we evaluate in detail the applicability of this 1D modelling approach to realistic three-dimensional (3D) simulated seismic wavefields in shallow sedimentary basins. Linear-viscoelastic 1D SRA predictions using two types of input motions that are commonly used in practice—rock outcrop and in-column motions, are compared with the reference true site response results from 3D earthquake simulations in terms of various measures in the frequency and time domain. It is shown that the horizontal motion in the 3D seismic wavefield exhibits dominant shear wave propagation phenomenon, while the vertical motion is a combined effect of compressional and shear waves and can be over-predicted by the 1D approach when the incident seismic waves are inclined. Direct evidence of the wave refraction process that leads to the vertical motion over-prediction is provided. 1D SRA with in-column inputs can yield motions that have significantly longer duration compared to the true 3D site response solution due to trapped waves, casting in doubt the frequent need for increased soil damping in existing site studies to compensate for wave attenuation due to scattering alone. Sensitivity investigation on the increase of soil profile damping by a multiplier D mul shows D mul values compatible with those found in the literature for both horizontal and vertical motions. It is shown that the level of D mul optimized for a best match of the spectral acceleration is dependent on the characteristic of the input motion and a larger D mul is typically required for the vertical component. In contrast, 1D SRA with outcrop motions predicts motions with shorter significant duration due to its inability to capture the basin-edge generated surface waves. A suite of ground motion simulations was performed to assess the sensitivity of the observations to the basin geologic structure including the velocity gradient, rock-basin impedance contrast and basin depth. The analysis results show that the accuracy of the simplified 1D procedure is dependent on the wavefield composition of both the input motions and the true 3D site response solution. While the horizontal motions in shallow sedimentary basins can, to the first order, be reasonably captured by the simplified 1D approach, 1D SRA for the vertical component is in general not reliable and contributions from inclined shear waves should be accounted for in site-specific evaluation of the vertical design ground motion.

1D assumption↗

Insight into the nanostructure of “water in salt” solutions: A SAXS/WAXS study on imide-based lithium salts aqueous solutions

"Water-in-salt " electrolyte (WISE) series have been studied for lithium-ion batteries and supercapacitor applications, but so far, most of the focus has been on the LiTFSI salt-based systems. Herein, we used small-angle X-ray scattering/wide-angle X-ray scattering (SAXS/WAXS) and molecular dynamics (MD) simulation to investigate the solvation structure of a series of lithium salts with four different symmetric anions: (bis(fluoro sulfonyl)imide (FSI), bis(trifluoromethane sulfonyl)imide (TFSI), bis(pentafluoroethane sulfonyl) imide (BETI) and bis(nonafluorobutane sulfonyl)imide (BNTI)), which have similar parent structures but different lengths of the fluorocarbon chains. Two competing structures were found in the four lithium salts aqueous solutions: anion solvated structure and anion network. The anion network plays a crucial role in obtaining a stable and enlarged electrochemical window. The d spacing of the anion solvated structure follows a linear correlation with the number of carbons in the fluorocarbon chains and an exponential correlation with the concentrations. Further, we also observed that the transition from one structure to another is predominantly controlled by the salt volume fraction for all imide-based aqueous solutions. This work provides a systematic study of the atomistic scale structures of a series of imide-based lithium salt aqueous solutions that could extend the knowledge of WIS electrolytes.

25 ENERGY STORAGE↗

Extreme Fermi Surface Smearing in a Maximally Disordered Concentrated Solid Solution

We show that the Fermi surface can survive the presence of extreme compositional disorder in the equiatomic alloy Ni 0.25 Fe 0.25 Co 0.25 Cr 0.25 . Our high-resolution Compton scattering experiments reveal a Fermi surface which is smeared across a significant fraction of the Brillouin zone (up to 40% of $\frac{2π}{a}$). The extent of this smearing and its variation on and between different sheets of the Fermi surface have been determined, and estimates of the electron mean free path and residual resistivity have been made by connecting this smearing with the coherence length of the quasiparticle states.

36 MATERIALS SCIENCE↗

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Correlated characterization of 20 Ne-implanted targets using nuclear reaction analysis, Rutherford backscattering spectrometry, and ion transport modeling

In this article, we present the preparation and characterization of a large sample of implanted noble gas targets for use in precision nuclear astrophysics measurements with intense proton beams. Tantalum and titanium backings were prepared using wet-acid etching, outgassed via resistive heating, and implanted with 20 Ne + beams from differing ion sources. These experimental targets were investigated using both nuclear reaction analysis techniques on the 1169-keV resonance in 20 Ne(p, $\gamma$) 21 Na and Rutherford backscattering spectrometry analysis with 2-MeV α-particle beams. Results from these analyses reveal small target-to-target variations in stoichiometry, while exhibiting excellent agreement independent of ion-beam analysis method. We also present a self-consistent validation of the nuclear reaction analysis results using ion transport simulations in TRIM-2013 that rely on input parameters from SIMNRA scattering-yield fits to Rutherford backscattering spectra. In addition to a complete description of the implantation profile, this analysis method provides an alternate solution for characterizing a large sample of implanted targets when no suitable resonances are available for nuclear reaction analysis.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Resonant Inelastic X-ray Scattering Calculations of Transition Metal Complexes Within a Simplified Time-Dependent Density Functional Theory Framework

We present a time-dependent density functional theory (TDDFT) approach to compute the light-matter couplings between two different manifolds of excited states relative to a common ground state in the context of 4d transition metal systems. These quantities are the necessary ingredients to solve the Kramers-Heisenberg (KH) equation for resonant inelastic X-ray scattering (RIXS) and several other types of two-photon spectroscopies. The procedure is based on the pseudo-wavefunction approach, where the solutions of a TDDFT calculation can be used to construct excited-state wave- functions, and on the restricted energy window approach, where a manifold of excited states can be rigorously defined based on the energies of the occupied molecular orbitals involved in the excitation process. Thus, the present approach bypasses the need to solve the costly TDDFT quadratic-response equations. We illustrate the applicability of the method to 4d transition metal molecular complexes by calculating the 2p4d RIXS maps of three representative ruthenium complexes and comparing them to experimental results. The method can capture all the experimental features in all three complexes to allow the assignment of the experimental peaks, and relative energies correct to within 0.6 eV at the cost of two independent TDDFT calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Suppressing Phase Segregation and Improving Stability in Mixed-Halide Perovskites through Spinel Oxide-Directed Epitaxy

Mixed-cation mixed-halide perovskite compositions are essential for achieving the required bandgaps for high-efficiency multijunction photovoltaics, yet their stability remains limited by interfacial defects, phase segregation, and degradation. Here, we introduce spinel oxides as a new family of lattice-matched substrates that enable crystalline, phase-pure, compositionally-uniform, bromide-rich perovskite film growth. The effect of spinel oxides is two-fold: reducing defects at the bottom interface by templating film growth and inducing beneficial compressive strain through mismatch-dependent substrate-perovskite lattice coupling. Spinel oxide substrates facilitate growth of highly crystalline films and eliminate detrimental secondary phases across thicknesses. Using grazing incidence X-ray diffraction, X-ray fluorescence, cathodoluminescence–scanning electron microscopy, cryogenic photoluminescence, and density functional theory, we reveal that Mg-halide bonds at the bottom interface induce lattice mismatch-dependent compressive strain that suppresses halide segregation and further reduces defect formation. In addition, films grown on spinel oxides maintain over 87% of the perovskite phase after 12 h under 100% relative humidity, as monitored by in situ grazing incidence wide-angle X-ray scattering (GIWAXS), compared to less than 70% for control samples. This work extends lattice matching from vapor-deposited epitaxial semiconductors to solution-processed halide perovskites to establish a broadly applicable strategy for defect suppression, phase homogenization, and long-term stability. Based on the fundamental science explored here, we set the stage for the development of lattice-matched spinel oxide charge transport layers to be integrated into perovskite solar cells and other optoelectronic devices.

36 MATERIALS SCIENCE↗

Ab initio study of mechanical and thermal properties of GeTe-based and PbSe-based high-entropy chalcogenides

GeTe-based and PbSe-based high-entropy compounds have outstanding thermoelectric (TE) performance and crucial applications in mid and high temperatures. Recently, the optimization of TE performance of high-entropy compounds has been focused on reducing thermal conductivity by strengthening the phonon scattering process to improve TE performance. We report a first-principles investigation on nine GeTe-based high-entropy chalcogenide solid solutions constituted of eight metallic elements (Ag, Pb, Sb, Bi, Cu, Cd, Mn, and Sn) and 13 PbSe-based high-entropy chalcogenide solid solutions: Pb 0.99-y Sb 0.012 Sn y Se 1-2x Te x S x (x = 0.1, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, and y = 0) and Pb 0.99-y Sb 0.012 Sn y Se 1-2x Te x S x (y = 0.05, 0.1, 0.15, 0.2, 0.25 and x = 0.25). We have investigated the mechanical properties focusing on Debye temperature (Θ D ), thermal conductivity (κ), Grüneisen parameter (γ α ), dominant phonon wavelength (λ dom ), and melting temperature (T m ). We find that the lattice thermal conductivity is significantly reduced when GeTe is alloyed into the following compositions: Ge 0.75 Sb 0.13 Pb 0.12 Te, Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Bi 0.01 Te, and Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Mn 0.05 Bi 0.01 Te. This reduction is due to the mass increase and strain fluctuations. The results also show that Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Bi 0.01 Te solid solution has the lowest Young’s modulus (30.362 GPa), bulk and shear moduli (18.626 and 12.359 GPa), average sound velocity (1653.128 m/sec), Debye temperature (151.689 K), lattice thermal conductivity (0.574 W.m –1 .K –1 ), dominant phonon wavelength (0.692 Å), and melting temperature (535.91 K). Moreover, Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Bi 0.01 Te has the highest Grüneisen parameter with a reduced and temperature-independent lattice thermal conductivity. The positive correlation between Θ D and κ is revealed. Alloying of PbSe-based high-entropy by Sb, Sn, Te, and S atoms at the Se and Pb sites resulted in much higher shear strains resulted in the reduction of phonon velocity, a reduced Θ D , and a lower lattice thermal conductivity.

74 ATOMIC AND MOLECULAR PHYSICS↗

Panorama of new-physics explanations to the MiniBooNE excess

The MiniBooNE low-energy excess stands as an unexplained anomaly in short-baseline neutrino oscillation experiments. It has been shown that it can be explained in the context of dark sector models. Here, we provide an overview of the possible new-physics solutions based on electron, photon, and dilepton final states. We systematically discuss the various production mechanisms for dark particles in neutrino-nucleus scattering. Our main result is a comprehensive fit to the MiniBooNE energy spectrum in the parameter space of dark neutrino models, where short-lived heavy neutral leptons are produced in neutrino interactions and decay to e + e - pairs inside the detector. For the first time, other experiments will be able to directly confirm or rule out dark neutrino interpretations of the MiniBooNE low-energy excess.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Variance Reduction within Implicit Monte Carlo Thermal Radiation Transport using the Local Importance Function Transform [Slides]

System of equations derived by Fleck and Cummings to model time-dependent thermal radiative transfer (TRT) problems: Solution of radiation specific intensity (I), non-linearly coupled to material internal energy (U); Absorption and re-emission approximated by effective scattering events. Useful for high-energy density physics simulations: i.e., astrophysics, inertial confinement fusion (ICF). Whereas deterministic methods are fully discretized and free of statistical noise, Monte Carlo methods allow for dynamic sampling of the phase space at the price of statistical noise; Monte Carlo methods are also characterized by a slow $\frac{1}{√Ν}$ convergence rate.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DE-SC0021158: Additive-Assisted Preparation of Multinary Halides

This final report summarizes our achievements under the project DE-SC0021158. Briefly, this project allowed us to synthesize using solution chemistry methods and study multinary metal halides. Furthermore, we showed that optical spectroscopy methods in combination with Small Angle X-ray Scattering (SAXS) and Electrospray Ionization Mass Spectrometry (ESI-MS) can be used to discover brand new optical and electronic materials in .

36 MATERIALS SCIENCE↗

Review: Real-space analyses of local dynamics in liquid using X-ray scattering

In this review, we advocate describing the liquid dynamics using the Van Hove correlation function, a temporal and spatial correlation function. Recent progress in X-ray optics and X-ray sources makes it possible to carry out inelastic and quasi-elastic x-ray scattering whose spectra can be converted into the dynamic correlation function in real space. We describe the basic concept of the Van Hove correlation function, how it is obtained from the X-ray scattering spectra using synchrotron X-rays and X-ray free electron lasers, and the atomic dynamics in water and aqueous salt solution.

Shinohara, Yuya↗