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At least 1,369 records · Page 76

Role of backbone strain in de novo design of complex α/β protein structures

Abstract We previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Complex pressure-temperature structural phase diagram of the honeycomb iridate Cu 2 IrO 3

Cu 2 IrO 3 is among the newest layered honeycomb iridates and a promising candidate to harbor a Kitaev quantum spin liquid state. Here, we investigate the pressure and temperature dependence of its structure through a combination of powder x-ray diffraction and x-ray absorption fine structure measurements, as well as ab initio evolutionary structure search. At ambient pressure, we revise the previously proposed C2/c solution with a related but notably more stable P2 1 /c structure. Pressures below 8 GPa drive the formation of Ir-Ir dimers at both ambient and low temperatures, similar to the case of Li 2 IrO 3 . At higher pressures, the structural evolution dramatically depends on temperature. Furthermore, a large discontinuous reduction of the Ir honeycomb interplanar distance is observed around 15 GPa at room temperature, likely driven by a collapse of the O-Cu-O dumbbell bonds. At 15 K, pressures beyond 20 GPa first lead to an intermediate phase featuring a continuous reduction of the interplanar distance, which then collapses at 30 GPa across yet another phase transition. However, the resulting structure around 40 GPa is not the same at room and low temperatures. Remarkably, the reduction in interplanar distance leads to an apparent healing of the stacking faults at room temperature, but not at 15 K. Possible implications on the evolution of electronic structure of Cu 2 IrO 3 with pressure are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Complex fermiology and electronic structure of antiferromagnet EuSnP

Throughout this work, we studied the electronic structure of a layered antiferromagnetic metal, EuSnP, in the paramagnetic and in the antiferromagnetic phase using angle-resolved photoemission spectroscopy (ARPES) alongside density-functional theory (DFT)-based first-principles calculations. The temperature dependence of the magnetic susceptibility measurements exhibits an antiferromagnetic transition at a Néel temperature of 21 K. Employing high-resolution ARPES, the valence-band structure was measured at several temperatures above and below the Néel temperature, which produced identical spectra independent of temperature. Through analysis of the ARPES results presented here, we attribute the temperature-independent spectra to the weak coupling of the Sn and P conduction electrons with Eu 4⁢ƒ states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Unraveling the Determinant Mechanisms in Flow-Mediated Crystal Growth and Phase Behaviors

To uncover the critical mechanisms responsible for mesoscopic level development during flow-mediated crystal growth, we develop a semi-two-way hydrodynamic coupled structural phase-field crystal formalism (HXPFC-s2). The new formalism, inspired by previous attempts at coupling hydrodynamic and phase-field crystal (PFC) equations, allows for studying mesoscopic flow-mediated crystallization at diffusive timescales pertinent to industrial applications. Unlike previous efforts, the devised coupling to the structural PFC (XPFC) equations allows generalization to more complex crystal structures through explicit parameterization of the direct correlation function (DCF). Utilizing the HXPFC-s2 formalism, we seek to uncover the determinant physical mechanisms in crystallization under simple shear flows by comparing temperature-driven crystallization to flow-mediated crystallization under varying flow-strengths. Parallels and deviations of under-cooling and flow-strength effects on crystal growth are drawn using the crystal cluster-size and system ordering time evolutions. In doing so, we identify scaling behaviors with a Peclet-like number, Pe∼, a critical Peclet-like number, Pe∼*, and flow-field-crystal plane-dependent interactions. Our findings may be relevant for controlling crystal growth and phase behaviors in flow applications.

Willis, L. Connor (ORCID:0009000961321848)↗

Sources of and Remedies for Removing Unwanted Reflections in Millimeter Wave Images of Complex SOFI-Covered Structures

In the recent years, continuous-wave (CW) near-field and lens-focused millimeter wave imaging systems have been effectively. used to demonstrate their utility for producing high-resolution images of metallic structures covered with spray on foam insulation (SOFI) such as the space shuttle external tank. These systems have produced images with a spatial resolution of approximately 2 mm at a frequency of 150 GHz, and can easily interrogate thin as well as thick SOFI (> 9") enabling detection and evaluation of flaws such as voids, disbands, delaminations and corrosion. These systems are relatively simple, inexpensive, easy-to-use, require little to no signal processing of the raw data, on-site friendly, real-time and small. However, for some specific structures a certain interference pattern may be superimposed on the produced images. Generally, this occurs when the SOFI surface is at a relatively significant angle with respect to the surface of the substrate (or other sub-structures) on which it is sprayed. Consequently, the reflection from the surface of the SOFI and that from the substrate (or sub-structure) coherently combine into an interference pattern as the SOFI surface is scanned. There are methods by which the influence of this unwanted interference can be reduced, such as the incorporation of an incidence angle and the proper use of signal polarization. This paper presents the basics of this problem and describes the use of the methods for reducing this unwanted influence through several specific examples. A discussion on how the use of a swept-frequency or pulsed method may also alleviate this problem is also presented.

Khakovsky, S.↗

PTT System Performance Evaluation in 3-D Imaging of AM Components

Additive manufacturing (AM, or 3D printing) for commercial nuclear energy applications is an emerging method for cost-efficient manufacturing aimed at replacing aging nuclear reactor parts and reducing costs for new construction. Because of the geometry of metallic structures of interest for nuclear applications, which consist of planar primitives with no symmetry of revolution, limited options are available for non-destructive evaluation (NDE) either during or post manufacturing. Known material flaws in AM include low density regions consisting of nonsintered powder, which have to be detected to ensure the safety of long-term performance nuclear reactor components. As a solution to NDE of AM, we are developing pulsed thermal tomography (PTT) models and depth inversion algorithms for 3D imaging. PTT has many advantages because the method is non-contact and allows for in-service, NDE of AM nuclear reactor parts. By analyzing transients of surface temperature response due to internal thermal resistances, one can obtain 3D reconstructions of material effusivity using a unique inversion algorithm developed at Argonne. This study investigates the capability of PTT in imaging several AM structures fabricated from Inconel 718 (IN718) feedstock. The AM structures have complex geometry, but do not have calibrated internal defects. The objective is to determine PTT settings, such as the total integration time, for imaging of representative AM structures. A new FLIR X8500sc IR camera with higher spatial resolution (1280x1024 at 181Hz frame rate) was integrated into the PTT laboratory setup. Software tools were developed to ensure compatibility of new camera files with legacy effusivity reconstruction codes. The new camera was used to obtain 3-D reconstructions of IN718 nozzle plate and a particle filter plate. The results demonstrate the capability of PTT in 3- D imaging of complex geometry AM structures. Further, increased resolution imaging is achieved compared to prior results using older FLIR SC4000 IR camera. In addition, preliminary studies were conducted on developing image processing algorithms for automated detection of flaws. Initial demonstrations are shown for segmentation of PTT images of flat bottom hole (FBH) specimens. Imaging of FBH specimens was described in a prior report. Intermediate results demonstrated in this report will be developed further in detection of flaws in AM specimens.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Microfibril orientation and compositional heterogeneity in fiber and vessel cell walls of poplar xylem studied by AFM-IR and SFG spectroscopy

Understanding the structural organization of cellulose microfibrils (CMFs) within individual plant cell walls is essential for connecting cell wall architecture to its mechanical and physiological functions. However, due to the complex hierarchical structure and nanoscale heterogeneity of cell walls, it remains technically challenging to resolve detailed compositional and orientational information at subcellular levels of individual cell walls. This study investigates the internal 3D structure, chemical composition, and sublayer organization of fiber and vessel cell walls in the xylem tissue of a two-year-old field-grown hybrid poplar tree (Populus alba × P. glandulosa) using photothermal atomic force microscopy coupled with infrared spectroscopy (AFM-IR) and sum frequency generation (SFG) hyperspectral microscopy. AFM-IR provided nanoscale chemical imaging, revealing localized compositional heterogeneity, including variations between adjacent cell walls and transitional layers beyond the traditional S1, S2, and S3 sublayers. SFG microscopy revealed that CMFs in fiber walls are highly aligned along the stem axis, consistent with their role in mechanical support, while vessel cell walls exhibited slightly tilted CMFs, reflecting their function in hydraulic transport. Together, these results offer new insights into cell-type-specific CMF organization and compositional gradients in hybrid poplar xylem. These findings highlight the structural and chemical complexity of secondary cell walls in woody plants and demonstrate the value of AFM-IR and SFG spectroscopy in elucidating plant cell wall architecture.

60 APPLIED LIFE SCIENCES↗

Acoustic fatigue life prediction for non-linear structures

Using an approach based on a time domain analysis, a method of equivalent linearization is applied for an estimation of the strain response of complex nonlinear structures having nearly arbitrary complexity. Fatigue lives estimated for a nonlinear beam with random excitation using the approximate method were compared with results obtained using a conventional numerical simulation, yielding nearly identical results.

Sun, J. Q.↗

Effect of stress concentrations in composite structures

The goal of achieving a better understanding of the failure of complex composite structure is sought. This type of structure requires a thorough understanding of the behavior under load both on a macro and micro scale if failure mechanisms are to be understood. The two problems being studied are the failure at a panel/stiffener interface and a generic problem of failure at a stress concentration.

Babcock, G. D.↗