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At least 415 records · Page 23

Subpicosecond HI elimination in the 266 nm photodissociation of branched iodoalkanes

Here, the 266 nm photodissociation dynamics of 1-iodopropane and 2-iodopropane were studied using photofragment translational energy spectroscopy using vacuum ultraviolet (VUV) photoionization and electron impact ionization detection of products. The photochemistry of 1-iodopropane was found to be similar to that of iodomethane and iodoethane, with dominant production of I*( 2 P 1/2 ), and no evidence (<0.21%) for HI + alkene formation. Significantly different behavior was observed for 2-iodopropane, with dominant production of ground state I( 2 P 3/2 ), and a HI yield >10.5%. The anisotropy (β) parameters for all channels approached the limiting value of 2.0, indicating that 1,2-HI elimination occurs on subpicosecond timescales, like direct C–I bond fission, following excitation to 3 Q 0 . The HI translational energy and angular distributions were similar to those for I( 2 P 3/2 ), suggesting that motion of the heavy I atom in HI is largely derived from the repulsive nature of the 1 Q 1 surface correlating to R + I with the light H atom picked up by ground state I late in the exit channel producing highly vibrationally excited HI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photodissociation of iso-propoxy (i-C 3 H 7 O) radical at 248 nm

Photodissociation of the i-C 3 H 7 O radical is investigated using fast beam photofragment translational spectroscopy. Neutral i-C 3 H 7 O radicals are produced through the photodetachment of a fast beam of i-C 3 H 7 O - anions and are subsequently dissociated at 248 nm (5.0 eV). Furthermore, the dominant product channels are CH 3 + CH 3 CHO and OH + C 3 H 6 with some contribution from H + C 3 H 6 O. The CH 3 and H loss channels are attributed to dissociation on the ground electronic state of i-C 3 H 7 O, but in a nonstatistical manner because calculated RRKM dissociation rates exceed the rate of energy randomization. Translational energy and angular distributions for OH loss are consistent with ground state dissociation, but the branching ratio for this channel is considerably higher than predicted from RRKM rate calculations. Additionally, i-C 3 H 7 O undergoes three-body fragmentation to CH 3 + CH 3 + HCO and CH 3 + CH 4 + CO. These three-body channels are attributed to dissociation of i-C 3 H 7 O to CH 3 + CH 3 CHO, followed by secondary dissociation of CH 3 CHO on its ground electronic state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering endosomolytic nanocarriers of diverse morphologies using confined impingement jet mixing

The clinical translation of many biomolecular therapeutics has been hindered by undesirable pharmacokinetic (PK) properties, inadequate membrane permeability, poor endosomal escape and cytosolic delivery, and/or susceptibility to degradation. Overcoming these challenges merits the development of nanoscale drug carriers (nanocarriers) to improve the delivery of therapeutic cargo. Herein, we implement a flash nanoprecipitation (FNP) approach to produce nanocarriers of diverse vesicular morphologies by using various molecular weight PEG-bl-DEAEMA-co-BMA (PEG-DB) polymers. We demonstrated that FNP can produce uniform (PDI < 0.1) particles after 5 impingements, and that by varying the copolymer hydrophilic mass fraction, FNP enables access to a diverse variety of nanoarchitectures including micelles, unilamellar vesicles (polymersomes), and multi-compartment vesicles (MCVs). We synthesized a library of 2 kDa PEG block copolymers, with DEAEMA-co-BMA second block molecular weights of 3, 6, 12, 15, 20, and 30 kDa. All formulations were both pH responsive, endosomolytic, and capable of loading and cytosolically delivering small negatively charged molecules – albeit to different degrees. Using a B16.F10 melanoma model, we showcased the therapeutic potential of a lead FNP formulated PEG-DB nanocarrier, encapsulating the cyclic dinucleotide (CDN) cGAMP to activate the stimulator of interferon genes (STING) pathway in a therapeutically relevant context. Collectively, these data demonstrate that an FNP process can be used to formulate pH-responsive nanocarriers of diverse morphologies using a PEG-DB polymer system. As FNP is an industrially scalable process, these data address the critical translational challenge of producing PEG-DB nanoparticles at scale. Furthermore, the diverse morphologies produced may specialize in the delivery of distinct biomolecular cargos for other therapeutic applications, implicating the therapeutic potential of this platform in an array of disease applications.

36 MATERIALS SCIENCE↗

Dynamics of fluorinated imide-based ionic liquids using nuclear magnetic resonance techniques

There is increasing interest in studying molecular motions in ionic liquids to gain better insights into their transport properties and to expand their applications. Here, in this study, we have employed the fast field cycling relaxometry and pulsed field gradient nuclear magnetic resonance techniques to investigate the rotational and translational dynamics of fluorinated imide-based ionic liquids (ILs) at different temperatures. We have studied a total of six ILs composed of the 1-butyl-3-methylimidazolium cation ([BMIM] + ) combined with chemically modified analogs of the bis((trifluoromethyl)sulfonyl)imide anion ([NTf 2 ] − or [TFSI] − ). The primary objective of this paper is to broaden the understanding of how the anion's conformational flexibility, fluorination, and mass affect the molecular dynamics of cations and anions. Our results indicate that flexibility has the most significant impact on the rotational and translational motions of ions. Meanwhile, the effect of fluorination and mass is only relevant when conformational flexibility does not change significantly between the ILs being compared.

25 ENERGY STORAGE↗

A decay database of coincident γ–γ and γ–X -ray branching ratios for in-field spectroscopy applications

Current fieldable spectroscopy techniques often use single detector systems heavily impacted by interferences from intense background radiation fields. These effects result in low-confidence measurements that can lead to misinterpretation of the collected spectrum. To help improve interpretation of the fission products and short-lived radionuclides produced in a composite sample, a coincidence-database is being developed in support of a robust portable and X-ray coincidence detector system concurrently under development at the Pacific Northwest National Laboratory for in-field deployment. Hitherto, no database exists containing coincident γ–γ and γ–X-ray branching-ratio intensities on an absolute scale that will greatly enhance isotopic identification for in-field applications. As part of this project, software has been developed to parse all radioactive-decay data sets from the Evaluated Nuclear Structure Data File (ENSDF) archive to enable translation into a more useful JavaScript Object Notation (JSON) formats that more readily supports query-based data manipulation. The coincident database described in this work is the first of its kind and contains coincidence γ–γ and γ–X-ray intensities and their corresponding uncertainties, together with auxiliary metadata associated with each decay data set. The new JSON format provides a convenient and portable means of data storage that can be imported into analysis frameworks with relatively low overhead allowing for meaningful comparison with measured data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Too big, too small, or just right? A benchmark assessment of density functional theory for predicting the spatial extent of the electron density of small chemical systems

Multipole moments are the first-order responses of the energy to spatial derivatives of the electric field strength. The quality of density functional theory prediction of molecular multipole moments thus characterizes errors in modeling the electron density itself, as well as the performance in describing molecules interacting with external electric fields. However, only the lowest non-zero moment is translationally invariant, making the higher-order moments origin-dependent. Therefore, instead of using the 3 × 3 quadrupole moment matrix, we utilize the translationally invariant 3 × 3 matrix of second cumulants (or spatial variances) of the electron density as the quantity of interest (denoted by K). The principal components of K are the square of the spatial extent of the electron density along each axis. A benchmark dataset of the principal components of K for 100 small molecules at the coupled cluster singles and doubles with perturbative triples at the complete basis set limit is developed, resulting in 213 independent K components. The performance of 47 popular and recent density functionals is assessed against this Var213 dataset. Several functionals, especially double hybrids, and also SCAN and SCAN0 predict reliable second cumulants, although some modern, empirically parameterized functionals yield more disappointing performance. The H, Li, and Be atoms, in particular, are challenging for nearly all methods, indicating that future functional development could benefit from the inclusion of their density information in training or testing protocols.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Measurements of dynamic surface changes by digital holography for in situ plasma erosion applications

There are currently few viable diagnostic techniques for in situ measurement of plasma facing component erosion. Digital holography is intended to fill this gap. Progress on the development of single and dual CO 2 laser digital holography diagnostics for in situ plasma facing component erosion is discussed. The dual laser mode’s synthetic wavelength allows the measurable range to be expanded by a factor of ~400 compared to single laser digital holography. This allows the diagnostic to measure surface height changes of up to 4.5 μm in single laser mode and up to 2 mm in dual laser mode. Results include ex situ measurements of plasma eroded targets and also dynamic measurements of nm and μm scale motion of a target mounted on a precision translation stage. Dynamic measurements have successfully been made with the system operating in both single and dual laser modes, from ~50 nm to ~4 μm in single laser mode and up to ~400 μm in dual laser mode (limited only by the stage speed and camera acquisition duration). These results demonstrate the feasibility of using digital holography to characterize plasma facing component erosion dynamically, i.e., during plasma exposure. Results of proof-of-principle in situ digital holographic measurements of targets exposed to an electrothermal arc plasma source are presented.

Smith, Cary↗

Learning intermolecular forces at liquid–vapor interfaces

By adopting a perspective informed by contemporary liquid-state theory, we consider how to train an artificial neural network potential to describe inhomogeneous, disordered systems. Here, we find that neural network potentials based on local representations of atomic environments are capable of describing some properties of liquid-vapor interfaces but typically fail for properties that depend on unbalanced long-ranged interactions that build up in the presence of broken translation symmetry. These same interactions cancel in the translationally invariant bulk, allowing local neural network potentials to describe bulk properties correctly. By incorporating explicit models of the slowly varying long-ranged interactions and training neural networks only on the short-ranged components, we can arrive at potentials that robustly recover interfacial properties. We find that local neural network models can sometimes approximate a local molecular field potential to correct for the truncated interactions, but this behavior is variable and hard to learn. Generally, we find that models with explicit electrostatics are easier to train and have higher accuracy. We demonstrate this perspective in a simple model of an asymmetric dipolar fluid, where the exact long-ranged interaction is known, and in an ab initio water model, where it is approximated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Study of the water dynamics near hydrophilic, nanostructured CuO surfaces by quasielastic and inelastic neutron scattering

We have used quasielastic and inelastic neutron scattering to investigate the structure, dynamics, and phase transitions of water interacting with superhydrophilic CuO surfaces that not only possess a strong affinity for water but also a “grass-like” topography that is rough on both micro- and nanoscales. Here, we report quasielastic neutron scattering (QENS) measurements on two samples differing in water content at five temperatures below 280 K. The QENS spectra show water undergoing two different types of diffusive motion near the CuO surfaces: a “slow” translational diffusion occurring on a nanosecond time scale and a faster rotational motion. Further from the surfaces, there is “fast” translational diffusion comparable in rate to that of bulk supercooled water and the rotational motion occurring in the interfacial water. Analysis of the QENS spectra supports wetting of water to the CuO blades as seen in electron microscopy images. In addition, we observe an anomalous temperature dependence of the QENS spectra on cooling from 270 to 230 K with features consistent with a liquid–liquid phase transition. We suggest that the solvent-like properties of the coexisting bulk-like water in our CuO samples are a significant factor in determining the temperature dependence of the interfacial water’s dynamics. Our results are compared with those obtained from two well-studied substrate classes: (1) silicas that contain ordered cylindrical nanopores but have weaker hydrophilicity and (2) nanoparticles of other transition-metal oxides, such as TiO 2 , which share the strong hydrophilicity of our samples but lack their porosity.

36 MATERIALS SCIENCE↗

Lightweight and effective tensor sensitivity for atomistic neural networks

Atomistic machine learning focuses on the creation of models that obey fundamental symmetries of atomistic configurations, such as permutation, translation, and rotation invariances. In many of these schemes, translation and rotation invariance are achieved by building on scalar invariants, e.g., distances between atom pairs. There is growing interest in molecular representations that work internally with higher rank rotational tensors, e.g., vector displacements between atoms, and tensor products thereof. Here, we present a framework for extending the Hierarchically Interacting Particle Neural Network (HIP-NN) with Tensor Sensitivity information (HIP-NN-TS) from each local atomic environment. Crucially, the method employs a weight tying strategy that allows direct incorporation of many-body information while adding very few model parameters. We show that HIP-NN-TS is more accurate than HIP-NN, with negligible increase in parameter count, for several datasets and network sizes. As the dataset becomes more complex, tensor sensitivities provide greater improvements to model accuracy. In particular, HIP-NN-TS achieves a record mean absolute error of 0.927 $\frac{\text{kcal}}{\text{mol}}$ for conformational energy variation on the challenging COMP6 benchmark, which includes a broad set of organic molecules. We also compare the computational performance of HIP-NN-TS to HIP-NN and other models in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optical design for the single crystal neutron diffractometer Pioneer

Pioneer is a single-crystal neutron diffractometer optimized for small-volume samples and weak signals at the Second Target Station at Oak Ridge National Laboratory. This paper presents the preliminary optical design progress, focusing on the rationale behind key design choices. It covers the T 0 and bandwidth disk choppers, guide and beam control system, incident-beam polarizer, scattering beam collimators, and additional strategies. The chopper locations are selected to maximize neutron transport while taking advantage of standardized shielding structures. To accommodate the maintenance shield, operational shutter, and polarizing V-cavity, the guide design includes significant gaps. When these optical components are moved out of the beam path, oversized collimators, rather than guides, will be translated in. Pioneer will utilize slit packages to control beam size and divergence and a translatable polarizing V-cavity. Absorbing panels are strategically placed near the end station to minimize background. An oscillating radial collimator, operating in a shift mode, will be used with the vertical cylindrical detector, while a fixed multi-cone collimator will be used with the bottom flat detector. In conclusion, these collimators will enable the detection of weak signals when complex sample environments are used.

47 OTHER INSTRUMENTATION↗

Genome-wide role of codon usage on transcription and identification of potential regulators

Significance Codon usage bias, the preference for certain synonymous codons, is a feature of all genomes and plays an important role in determining gene expression levels. Surprisingly, in addition to its role in mRNA translation, codon usage was recently shown to regulate gene expression at the transcriptional level. In this study, our results suggest that codon usage influences transcription genome-wide independently of its effect on translation. By carrying out a large-scale genetic screen, we identified 18 factors participating in multiple transcriptional regulatory mechanisms involved in the codon usage-mediated transcriptional effects. Together, our study establishes a foundation for future mechanistic understanding of this gene regulatory phenomenon.

Zhao, Fangzhou↗

Cross-correlation analysis of X-ray photon correlation spectroscopy to extract rotational diffusion coefficients

Coefficients for translational and rotational diffusion characterize the Brownian motion of particles. Emerging X-ray photon correlation spectroscopy (XPCS) experiments probe a broad range of length scales and time scales and are well-suited for investigation of Brownian motion. While methods for estimating the translational diffusion coefficients from XPCS are well-developed, there are no algorithms for measuring the rotational diffusion coefficients based on XPCS, even though the required raw data are accessible from such experiments. In this paper, we propose angular-temporal cross-correlation analysis of XPCS data and show that this information can be used to design a numerical algorithm (Multi-Tiered Estimation for Correlation Spectroscopy [MTECS]) for predicting the rotational diffusion coefficient utilizing the cross-correlation: This approach is applicable to other wavelengths beyond this regime. We verify the accuracy of this algorithmic approach across a range of simulated data.

97 MATHEMATICS AND COMPUTING↗

Split aminoacyl-tRNA synthetases for proximity-induced stop codon suppression

Synthetic biology tools for regulating gene expression have many useful biotechnology and therapeutic applications. Most tools developed for this purpose control gene expression at the level of transcription, and relatively few methods are available for regulating gene expression at the translational level. Here, we design and engineer split orthogonal aminoacyl-tRNA synthetases (o-aaRS) as unique tools to control gene translation in bacteria and mammalian cells. Using chemically induced dimerization domains, we developed split o-aaRSs that mediate gene expression by conditionally suppressing stop codons in the presence of the small molecules rapamycin and abscisic acid. Furthermore, by activating o-aaRSs, these molecular switches induce stop codon suppression, and in their absence stop codon suppression is turned off. We demonstrate, in Escherichia coli and in human cells, that split o-aaRSs function as genetically encoded AND gates where stop codon suppression is controlled by two distinct molecular inputs. In addition, we show that split o-aaRSs can be used as versatile biosensors to detect therapeutically relevant protein–protein interactions, including those involved in cancer, and those that mediate severe acute respiratory syndrome-coronavirus-2 infection.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing Monte Carlo Workflows for Nuclear Reactor Analysis with Metamodel-Driven Modeling

Monte Carlo codes are essential components of many reactor physics simulation workflows as high-fidelity continuous-energy neutron transport solvers. Among Monte Carlo radiation transport codes, MCNP is particularly notable due to its diverse simulation capabilities, large user base, and long validation history. Despite being a powerful simulation tool, MCNP provides limited capabilities to allow automated execution, model transformation, or support for user-defined logic and abstractions that limit its compatibility with modern workflows. Here, to better integrate MCNP into a modern scientific workflow, we have developed an intuitive yet full-featured MCNP Application Program Interface (API) in Python, named MCNPy, which provides a specialized set of classes for MCNP input development. Moreover, to guarantee that our reading, writing, and modeling capabilities remain self-consistent (and to render the huge scope of the MCNP API manageable), we have adopted a strategy of model-driven software development in which a generalized model of the MCNP input format has been created. From this generalized model, or “metamodel,” problem-specific implementations such as an engine for input validation or a codebase for programmatic operations may be automatically generated. Since MCNPy primarily acts as a Python front-end to the underlying Java API that directly interfaces with the metamodel, it is intrinsically linked to the metamodel and thus remains maintainable. With MCNPy, users can programmatically read, write, and modify any syntactically valid MCNP input file regardless of its origin. These capabilities allow users to automate complicated tasks like design optimization and model translation for nuclear systems. As examples, this work demonstrates the use of MCNPy to find the critical radius of a plutonium sphere and to translate a 9000+ line MCNP input file into a corresponding OpenMC model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

N 2 vibrational excitation in atmospheric pressure ns pulse and RF plasma jets

Time-resolved N 2 vibrational temperature and translational–rotational temperature in quasi-two-dimensional atmospheric pressure plasma jets sustained by ns pulse and RF discharges in nitrogen/noble gas mixtures are measured by the broadband vibrational Coherent Anti-Stokes Raman Scattering (CARS) . The results indicate a much stronger vibrational excitation in the RF plasma jet, due to the lower reduced electric field and higher discharge power. In a ns pulse discharge in N 2 /He, N 2 vibrational temperature is significantly lower compared to that in N 2 /Ar, due to the more rapid vibration–translation (V–T) relaxation of nitrogen by helium atoms. In the RF plasma jets in N 2 /Ne and N 2 /Ar, the vibrational excitation increases considerably as the nitrogen fraction in the mixture is reduced. The experimental data in the RF plasma jet in N 2 /Ar jet are compared with the kinetic modeling predictions. The results indicate that nitrogen vibrational excitation in N 2 /Ar plasma jets with a small N 2 fraction in the mixture (several percent) is controlled primarily by electron impact, anharmonic vibration–vibration (V–V) pumping, and V–T relaxation by N atoms. In comparison, V–V energy transfer from the vibrationally excited molecules in the first excited electronic state, N 2 (A 3 Σ u + , v), which are generated primarily by the energy transfer from the metastable Ar atoms, has a minor effect on the vibrational populations of the ground electronic state, N 2 (X 1 Σ g + , v). Although the discharge energy fraction going to electronic excitation is significant, the predicted quasi-steady-state N 2 (A 3 Σ u + ) number density, controlled by the energy pooling and quenching by N atoms, remains relatively low. Because of this, the net rate of N 2 (X 1 Σ g + ) vibrational excitation by the V–V energy transfer from N 2 (A 3 Σ u + ) is much lower compared to that by the direct electron impact. Furthermore, the results show that atmospheric pressure RF plasma jets can be used as sources of highly vibrationally excited N 2 molecules and N atoms.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Stability of exact solutions of the (2 + 1)-dimensional nonlinear Schrödinger equation with arbitrary nonlinearity parameter κ

In this work, we consider the nonlinear Schrödinger equation (NLSE) in 2+1 dimensions with arbitrary nonlinearity exponent κ in the presence of an external confining potential. Exact solutions to the system are constructed, and their stability as we increase the 'mass' (i.e., the L 2 norm) and the nonlinearity parameter κ is explored. Here we observe both theoretically and numerically that the presence of the confining potential leads to wider domains of stability over the parameter space compared to the unconfined case. Our analysis suggests the existence of a stable regime of solutions for all κ as long as their mass is less than a critical value M*(κ). Furthermore, we find that there are two different critical masses, one corresponding to width perturbations and the other one to translational perturbations. The results of Derrick's theorem are also obtained by studying the small amplitude regime of a four-parameter collective coordinate (4CC) approximation. A numerical stability analysis of the NLSE shows that the instability curve M*(κ) versus κ lies below the two curves found by Derrick's theorem and the 4CC approximation. In the absence of the external potential, κ = 1 demarcates the separation between the blowup regime and the stable regime. In this 4CC approximation, for κ < 1, when the mass is above the critical mass for the translational instability, quite complicated motions of the collective coordinates are possible. Energy conservation prevents the blowup of the solution as well as confines the center of the solution to a finite spatial domain. We call this regime the 'frustrated' blowup regime and give some illustrations. In an appendix, we show how to extend these results to arbitrary initial ground state solution data and arbitrary spatial dimension d.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A hybrid 3D/2D field response calculation for liquid argon detectors with PCB based anode plane

Liquid Argon Time Projection Chamber (LArTPC) technology is commonly utilized in neutrino detector designs. It enables detailed reconstruction of neutrino events with high spatial precision and low energy threshold. Its field response (FR) model describes the time-dependent electric currents induced in the anode-plane electrodes when ionization electrons drift nearby. An accurate and precise FR is a crucial input to LArTPC detector simulations and charge reconstruction. Established LArTPC designs have been based on parallel wire planes. It allows accurate and computationally economic two-dimensional (2D) FR models utilizing the translational symmetry along the direction of the wires. Recently, novel LArTPC designs utilize electrodes formed on printed circuit board (PCB) in the shape of strips with through holes. The translational symmetry is no longer a good approximation near the electrodes and a new FR calculation that employs regions with three dimensions (3D) has been developed. Extending the 2D models to 3D would be computationally expensive. Fortuitously, the nature of strips with through holes allows for a computationally economic approach based on the finite-difference method (FDM). In this paper, we present a new software package pochoir that calculates LArTPC field response for these new strip-based anode designs. This package combines 3D calculations in the volume near the electrodes with 2D far-field solutions to achieve fast and precise field response computation. We apply the resulting FR to simulate and reconstruct samples of cosmic-ray muons and 39 Ar decays from a Vertical Drift (VD) detector prototype operated at CERN. We find the difference between real and simulated data within 5%. Current state-of-the-art LArTPC software requires a 2D FR which we provide by averaging over one dimension and estimate that variations lost in this average are smaller than 7%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗