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At least 487 records · Page 27

Peridynamic elastic waves in two-dimensional unbounded domains: Construction of nonlocal Dirichlet-type absorbing boundary conditions

The focus of this paper is on application of peridynamics (PD) to propagation of elastic waves in unbounded domains. We construct absorbing boundary conditions (ABCs) derived from a semi-analytical solution of the PD governing equation at the exterior region. This solution is made up of a finite series of plane waves, as fundamental solutions (modes), which satisfy the PD dispersion relations. The modes are adjusted to transmit the energy from the interior region (near field) to the exterior region (far field). The corresponding unknown coefficients of the series are found in terms of the displacement field at a layer of points adjacent to the absorbing boundary. This is accomplished through a collocation procedure at subregions (clouds) around each absorbing point. The proposed ABCs offer appealing advantages, which facilitate their application to PD. They are of Dirichlet-type, hence their implementation is relatively simple as no derivatives of the field variables are required. They are constructed in the time and space domains and thus application of Fourier and Laplace transforms, cumbersome for nonlocal models, is not required. At the discrete level, the modes satisfy the same numerical dispersion relations of the near field, which makes the far-field solution compatible with that of the near field. We scrutinize the performance of the proposed ABCs through several examples. So our investigation shows that the proposed ABCs perform stably in time with an appropriate level of accuracy even in problems characterized by highly-dispersive propagating waves, including crack propagation in semi-unbounded brittle solids.

42 ENGINEERING↗

Bayesian prior construction for uncertainty quantification in first-principles statistical mechanics

First-principles statistical mechanics enables the prediction of thermodynamic and kinetic properties of materials, but is computationally expensive. Many approaches require surrogate models to calculate energies within Monte Carlo or molecular dynamics simulations. Inexpensive surrogates such as cluster expansions enable otherwise intractable calculations by interpolating data from higher accuracy methods, such as Density Functional Theory (DFT). Surrogate models introduce uncertainty into downstream calculations, in addition to any uncertainty inherent to DFT calculations. Bayesian frameworks address this by quantifying uncertainty and incorporating expert knowledge through priors. However, constructing effective priors remains challenging. This work introduces and describes practical strategies for building Bayesian cluster expansions, focusing on basis truncation, hyperparameter selection, and ground state replication. We analyze multiple basis truncation schemes, compare cross-validation to the evidence-approximation for hyperparameter optimization, and provide methods to find and enforce ground-state-preserving models through priors. Additionally, we compare the uncertainties between different approximations to DFT (LDA, PBE, SCAN) against the uncertainty introduced with the use of cluster expansion surrogate models. These approaches are demonstrated on the BCC Li x Mg 1-x and Li x Al 1-x alloys, which are both of interest for solid-state Li batteries. Our results provide guidelines for constructing and utilizing Bayesian cluster expansions, thereby improving the transparency of materials modeling. Furthermore, the approaches and insights developed in this work can be transferred to a wide range of cluster expansion surrogate models, including the atomic cluster expansion and related machine-learned interatomic potential architectures.

Alloy theory↗

Global warming potential estimates of mass timber constructions beyond the first life: A dynamic radiative forcing modeling approach

In the face of a warming planet, steps must be taken to reduce the greenhouse gas emissions (GHG) associated with our building industry, which is a significant contributor to global emissions. Large, prefabricated wood elements such as mass timber panels (MTP) have great potential to achieve these reductions as they help displace high-embodied‑carbon materials like concrete and steel. Furthermore, storing the wood's biogenic carbon in buildings benefits the climate because it delays the eventual release of the carbon into the atmosphere. While these climate impacts have been assessed for the construction phase of mass timber buildings, relatively few life cycle assessment (LCA) studies have evaluated the climate impacts for the buildings' end-of-life (EOL) phase. This research estimates the climate impacts of four EOL scenarios for MTP: reusing as MTP, recycling into particleboard, incinerating, and landfilling. Using dynamic radiative forcing modeling and factoring in temporal GHG emissions and biogenic carbon storage, the global warming potential impacts are calculated for construction, deconstruction, and EOL processing of hybrid mass timber buildings in the U.S. Pacific Northwest for 160 years (GWP 160 ). The 160-year temporal scale used in this paper is an arbitrary scale, with the first 80 years being the assumed life of the building, followed by a series of reuse, recycle, or disposal scenarios over the second 80 years of that temporal scale. Of the four EOL scenarios considered in this paper, the ‘reuse’ scenario has the lowest net GWP 160 impact (calculated by summing the GWP 160 and carbon storage benefits, i.e., GWP$^{bioCS}_{160}$ ), emerging as a climate-preferred scenario, followed by ‘landfill’, ‘incinerate’, and ‘recycle’ scenarios. The lower net GWP 160 impact associated with the reuse scenario is due to the low fossil carbon emissions during EOL processing, as well as the biogenic carbon storage benefits. The results of this study also highlight the importance of efficient reuse and recycling strategies for wood in MTP.

42 ENGINEERING↗

Construction of 3D MHD pressure drop correlation and flow characterization in the contraction region of a fusion blanket manifold

Inlet and outlet manifolds are typical components of liquid metal (LM) blanket designs of a fusion power reactor to be used to distribute the LM flow into breeding channels and collect it at the exit of the blanket. High pressure loss in the magnetohydrodynamic (MHD) flows featuring abrupt geometrical changes is one of the main feasibility issues of such designs. Recently, optimization studies were conducted to construct 3D MHD pressure drop correlations for a LM flow in an electrically insulating manifold with gradual expansion. Here, the 3D computational approach developed in that study is applied to the outlet manifold featuring gradual contraction. A systematic analysis was performed with a total number of 135 flow cases computed with COMSOL Multiphysics for Hartmann numbers 1000 < Ha < 10,000, Reynolds numbers 100 < Re < 12,000, and contraction angles 45° < θ < 75° for a fixed contraction ratio of 4. The effects of Ha, Re and θ on the flow recirculation, development length and the total pressure drop were carefully examined. A linear regression analysis was used to determine the power rule of pressure drop coefficient k related to Ha and Re, demonstrating a good match with the Ludford layer theory. Eventually, a correlation for the 3D MHD pressure drop coefficient was constructed as a function of Ha, Re and θ. Further, the results were compared against the inlet manifold. It was found that the flow in the inlet manifold exhibits larger recirculation zones. In the investigated range of Ha, Re and θ, the pressure drop coefficient k of the LM MHD flow in the gradual contraction is only slightly lower (< 8 %) than that in the gradual expansion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measuring changes in environmental radiological background from construction of an advanced nuclear reactor testing facility

We present a method to survey and track changes in the environmental radiological background during the construction and operation of advanced nuclear reactor facilities. We discuss the results of two surveys of the environmental gamma-radiation background at NEXT Lab, an advanced nuclear reactor research facility on the campus of Abilene Christian University, prior to the introduction of radioactive material. In both surveys, the observed radiation dosage rates are low, with the highest rates at 15% of the average total radiation dosage rate for the United States. We observe ≈20% changes in the radiological background of the property in locations where the environment was changed by construction and ≈20% variations within the facilities correlated with variations in building materials.

Environment↗

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Nuclear physics without high-momentum potentials: Constructing the nuclear effective interaction directly from scattering observables

The traditional approach to nuclear physics encodes phase shift information in a nucleon-nucleon (NN) potential, producing a nucleon-level interaction that captures the sub-GeV consequences of QCD. A further reduction to the nuclear scale is needed to produce an effective interaction for soft Hilbert spaces, such as those employed in the shell model. Here we describe an alternative construction of the effective interaction that is simple and quite precise, proceeding from the QCD scale directly to the nuclear scale. This eliminates the need for constructing and renormalizing the high-momentum NN potential. Instead, continuum phase shifts and mixing angles are used directly at the nuclear scale. The method exploits the analytic continuity in energy of HOBET (Harmonic-Oscillator-Based Effective Theory) to connect bound states to continuum solutions at specific energies. The procedure is systematic, cutoff independent, and convergent, yielding keV accuracy at NNLO or N 3 LO, depending on the channel. Lepage plots are provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Direct construction of optimized stellarator shapes. Part 2. Numerical quasisymmetric solutions

Quasisymmetric stellarators are appealing intellectually and as fusion reactor candidates since the guiding-centre particle trajectories and neoclassical transport are isomorphic to those in a tokamak, implying good confinement. Previously, quasisymmetric magnetic fields have been identified by applying black-box optimization algorithms to minimize symmetry-breaking Fourier modes of the field strength $B$ . Here, instead, we directly construct magnetic fields in cylindrical coordinates that are quasisymmetric to leading order in the distance from the magnetic axis, without using optimization. The approach involves solution of a one-dimensional nonlinear ordinary differential equation, originally derived by Garren & Boozer ( Phys. Fluids B, vol. 3, 1991, p. 2805). We illustrate the usefulness and accuracy of this optimization-free approach by providing the results of this construction as input to the codes VMEC and BOOZ_XFORM, confirming the purity and scaling of the magnetic spectrum. The space of magnetic fields that are quasisymmetric to this order is parameterized by the magnetic axis shape along with three other real numbers, one of which reflects the on-axis toroidal current density, and another one of which is zero for stellarator symmetry. The method here could be used to generate good initial conditions for conventional optimization, and its speed enables exhaustive searches of parameter space.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Direct construction of optimized stellarator shapes. Part 3. Omnigenity near the magnetic axis

>The condition of omnigenity is investigated, and applied to the near-axis expansion of Garren & Boozer ( Phys. Fluids B, vol. 3 (10), 1991 a , pp. 2805–2821). Due in part to the particular analyticity requirements of the near-axis expansion, we find that, excluding quasi-symmetric solutions, only one type of omnigenity, namely quasi-isodynamicity, can be satisfied at first order in the distance from the magnetic axis. Our construction provides a parameterization of the space of such solutions, and the cylindrical reformulation and numerical method of Landreman & Sengupta ( J. Plasma Phys. , vol. 84 (6), 2018, 905840616); Landreman et al. ( J. Plasma Phys. , vol. 85 (1), 2019, 905850103), enables their efficient numerical construction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Modified Winterbottom Construction Including Boundaries

There has been extensive work on the equilibrium shape of isolated nanoparticles with internal boundaries, and also single crystals on substrates. Surprisingly, almost shockingly, there has been very little work on the equilibrium shape of particles with internal boundaries on substrates. Here in this paper, the general solution is given for the configuration of particles which contain twin and other grain boundaries on a flat substrate, which can be applied to any polycrystalline or multiphase nanoparticle configuration. The solution is based upon combining the established modified-Wulff construction that has been extensively validated for twinned particles with the Winterbottom construction for single particles on a substrate. The solution is illustrated for the specific case of five-fold multiply twinned particles. Good agreement is observed between both existing experimental data in the literature as well as some experimental data included within this work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Insight into a Sixteen Cyanine Dye Construct via Exciton–Exciton Annihilation

Molecular (dye) aggregates play a prominent role in light harvesting and are of interest in quantum information science; however, there are limited reports hat programmably assemble many (>4) dye aggregates featuring strong coupling and exciton delocalization. Using oligonucleotides with four Cy5s covalently linked in series along the phosphate backbone, we bring four, eight, and sixteen Cy5s in close proximity by assembling four-armed junctions. We elucidate their structure via gel electrophoresis and steady-state and transient optical spectroscopy. We find that Cy5 has a strong propensity to form tetramer clusters, where the exciton is delocalized over all four Cy5s, that the exciton is not delocalized beyond tetramer clusters in the eight and sixteen Cy5 constructs, and that the sixteen Cy5 construct may consist of pairs of tetramer clusters that are isolated from one another. Many-dye aggregates such as these may serve useful as antennae for their intense light absorption and spatially directed energy transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phthalocyanine Precursors To Construct Atomically Dispersed Iron Electrocatalysts

Carbon materials embedded with atomically dispersed metal sites have recently demonstrated intriguing performance as electrocatalysts. However, it remains challenging to construct abundant single metal atoms due to easy aggregation of metal species during the high-temperature synthesis. In this work, a facile method is developed to construct single iron atom electrocatalysts with high iron content by employing iron phthalocyanine (FePc) derivatives as metal precursors. FePc molecules are encapsulated into the zeolitic imidazolate frameworks (ZIFs), and the subsequent pyrolysis yields the catalysts. Cyano substitution on FePc (FePc(CN) 8 ) can facilitate introduction of phthalocyanine molecules and formation of active sites, thus affording higher activity for the oxygen reduction reaction than the FePc counterpart. It is also found that adding iron salt with FePc(CN) 8 can afford a better catalyst with enhanced surface Fe–N x content, which exhibits high activities with a half-wave potential of 0.910 and 0.811 V versus reversible hydrogen electrode in alkaline and acidic conditions, respectively. Moreover, FePc(CN) 8 /ZIF-derived catalyst exhibits high selectivities and good activities for carbon monoxide production in the carbon dioxide reduction reaction (CO 2 RR). The bulk Fe–N x sites are found to be more stable than the surface Fe–N x sites possibly due to the improved desorption of carbon monoxide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rapid Construction of Fe–Co–Ni Composition-Phase Map by Combinatorial Materials Chip Approach

100 nm thick Fe-Co-Ni materials chips were prepared and isothermally annealed at 500, 600 and 700oC, respectively. Pixel-by-pixel composition and structural mapping was performed by micro-beam X-ray at synchrotron light source. Diffraction images were recorded at a rate of 1 pattern/s. The XRD patterns were automatically processed, phase-identified and categorized by hierarchical clustering algorithm to construct the composition-phase map. Furthermore, the resulting maps are consistent with corresponding isothermal sections reported in the ASM Alloy Phase Diagram DatabaseTM, verifying the effectiveness of the present approach in phase diagram construction.

36 MATERIALS SCIENCE↗

Bottlebrush Polymers at Liquid Interfaces: Assembly Dynamics, Mechanical Properties, and All-Liquid Printed Constructs

Bottlebrush polymer surfactants (BPSs), formed by the interfacial interactions between bottlebrush polymers (BPs) with poly(acrylic acid) side chains dissolved in an aqueous phase and amine-functionalized ligands dissolved in the oil phase, assemble and bind strongly to the fluid-fluid interface. The ratio between N BB (backbone degree of polymerization) and N SC (side chain degree of polymerization) defines the initial assembly kinetics, interface packing efficiency, and stress relaxation. The equilibrium interfacial tension (γ) increases when N BB < N SC , but decreases when N BB $\gg$ N SC , correlating to a pronounced change in the effective shape of the BPs from being spherical to worm-like structures. The apparent surface coverage (ASC), i.e., the interfacial packing efficiency, decreases as N BB increases. The dripping-to-jetting transition of an injected polymer solution, as well as fluorescence recovery after photobleaching experiments, revealed faster initial assembly kinetics for BPs with higher N BB . Furhter, Euler buckling of BPS assemblies with different N BB values was used to characterize the stress relaxation behavior and bending modulus. The stress relaxation behavior was directly related to the ASC, reflecting the strong influence of macromolecular shape on packing efficiency. The bending modulus of BPSs decreases for N BB < N SC , but increased when N BB $\gg$ N SC , showing the effect of molecular architecture and multisite anchoring. All-liquid printed constructs with lower N BB BPs yielded more stable structured liquids, underscoring the importance of macromolecular packing efficiency at fluid interfaces. Overall, this work elucidates fundamental relationships between nanoscopic structures and macroscopic properties associated with various bottlebrush polymer architectures, which translate to the stabilization of all-fluidic printed constructs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Automated Construction of Artificial Lattice Structures with Designer Electronic States

Manipulating matter with a scanning tunneling microscope (STM) enables the creation of atomically defined artificial structures that host designer quantum states. However, the time-consuming nature of the manipulation process, coupled with the sensitivity of the STM tip, constrains the exploration of diverse configurations and limits the size of the designed features. In this study, we present a reinforcement learning (RL)-based framework for creating artificial structures by spatially manipulating carbon monoxide (CO) molecules on a copper substrate by using the STM tip. The automated workflow combines molecule detection and manipulation, employing deep-learning-based object detection to locate CO molecules and linear assignment algorithms to allocate these molecules to designated target sites. We initially perform molecule maneuvering based on randomized parameter sampling for sample bias, tunneling current set point, and manipulation speed. This data set is then structured into an action trajectory used to train an RL agent. The model is subsequently deployed on the STM for real-time fine-tuning of the manipulation parameters during structure construction. Our approach incorporates path-planning protocols coupled with active drift compensation to enable atomically precise fabrication of structures with significantly reduced human input while realizing larger-scale artificial lattices with the desired electronic properties. Furthermore, using our approach, we demonstrate the automated construction of an extended artificial graphene lattice and confirm the existence of a characteristic Dirac point in its electronic structure. Further challenges regarding the RL-based structural assembly scalability are discussed.

Algorithms↗

Construction of a Compact Array of Microplasma Jet Devices and Its Application for Random Mutagenesis of Rhodosporidium toruloides

A small and efficient DNA mutation-inducing machine was constructed with an array of microplasma jet devices (7 × 1) that can be operated at atmospheric pressure for microbial mutagenesis. Using this machine, we report disruption of a plasmid DNA and generation of mutants of an oleaginous yeast Rhodosporidium toruloides. Specifically, a compact-sized microplasma channel (25 × 20 × 2 mm 3 ) capable of generating an electron density of greater than 10 13 cm –3 was constructed to produce reactive species (N 2 *, N 2 +, O, OH, and H α ) under helium atmospheric conditions to induce DNA mutagenesis. The length of microplasma channels in the device played a critical role in augmenting both the volume of plasma and the concentration of reactive species. First, we confirmed that microplasma treatment can linearize a plasmid by creating nicks in vitro. Second, we treated R. toruloides cells with a jet device containing 7 microchannels for 5 min; 94.8% of the treated cells were killed, and 0.44% of surviving cells showed different colony colors as compared to their parental colony. Microplasma-based DNA mutation is energy-efficient and can be a safe alternative for inducing mutations compared to conventional methods using toxic mutagens. In conclusion, this compact and scalable device is amenable for industrial strain improvement involving large-scale mutagenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Searching for the rules that govern hadron construction

Just as quantum electrodynamics describes how electrons are bound in atoms by the electromagnetic force, mediated by the exchange of photons, quantum chromodynamics (QCD) describes how quarks are bound inside hadrons by the strong force, mediated by the exchange of gluons. QCD seems to allow hadrons constructed from increasingly many quarks to exist, just as atoms with increasing numbers of electrons exist, yet such complex constructions seemed, until recently, not to be present in nature. In this paper, we describe advances in the spectroscopy of mesons that are refining our understanding of the rules for predicting hadron structure from QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators

Abstract The ability of bacteria to sense specific molecules within their environment and trigger metabolic responses in accordance is an invaluable biotechnological resource. While many transcription factors (TFs) mediating such processes have been studied, only a handful have been leveraged for molecular biology applications. To expand the repertoire of biotechnologically relevant sensors we present a strategy for the construction and testing of chimeric TF libraries, based on the fusion of highly soluble periplasmic binding proteins (PBPs) with DNA-binding domains (DBDs). We validate this concept by constructing and functionally testing two unique sense-and-respond regulators for benzoate, an environmentally and industrially relevant metabolite. This work will enable the development of tailored biosensors for novel synthetic regulatory circuits.

59 BASIC BIOLOGICAL SCIENCES↗