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At least 1,387 records · Page 77

Role of Conserved Proline Residues in Human Apolipoprotein A-IV Structure and Function

Apolipoprotein (apo)A-IV is a lipid emulsifying protein linked to a range of protective roles in obesity, diabetes, and cardiovascular disease. It exists in several states in plasma including lipid-bound in HDL and chylomicrons and as monomeric and dimeric lipid-free/poor forms. Our recent x-ray crystal structure of the central domain of apoA-IV shows that it adopts an elongated helical structure that dimerizes via two long reciprocating helices. A striking feature is the alignment of conserved proline residues across the dimer interface. We speculated that this plays important roles in the structure of the lipid-free protein and its ability to bind lipid. Here we show that the systematic conversion of these prolines to alanine increased the thermodynamic stability of apoA-IV and its propensity to oligomerize. Despite the structural stabilization, we noted an increase in the ability to bind and reorganize lipids and to promote cholesterol efflux from cells. The novel properties of these mutants allowed us to isolate the first trimeric form of an exchangeable apolipoprotein and characterize it by small-angle x-ray scattering and chemical cross-linking. Here, the results suggest that the reciprocating helix interaction is a common feature of all apoA-IV oligomers. We propose a model of how self-association of apoA-IV can result in spherical lipoprotein particles, a model that may have broader applications to other exchangeable apolipoprotein family members.

59 BASIC BIOLOGICAL SCIENCES↗

Recognition of the β-lactam carboxylate triggers acylation of Neisseria gonorrhoeae penicillin-binding protein 2

Resistance of Neisseria gonorrhoeae to extended-spectrum cephalosporins (ESCs) has become a major threat to human health. The primary mechanism by which N. gonorrhoeae becomes resistant to ESCs is by acquiring a mosaic penA allele, encoding penicillin-binding protein 2 (PBP2) variants containing up to 62 mutations compared with WT, of which a subset contribute to resistance. To interpret molecular mechanisms underpinning cephalosporin resistance, it is necessary to know how PBP2 is acylated by ESCs. In this work, we report the crystal structures of the transpeptidase domain of WT PBP2 in complex with cefixime and ceftriaxone, along with structures of PBP2 in the apo form and with a phosphate ion bound in the active site at resolutions of 1–7-1.9 Å. These structures reveal that acylation of PBP2 by ESCs is accompanied by rotation of the Thr-498 side chain in the KTG motif to contact the cephalosporin carboxylate, twisting of the β3 strand to form the oxyanion hole, and rolling of the β3–β4 loop toward the active site. Recognition of the cephalosporin carboxylate appears to be the key trigger for formation of an acylation-competent state of PBP2. The structures also begin to explain the impact of mutations implicated in ESC resistance. In particular, a G545S mutation may hinder twisting of β3 because its side chain hydroxyl forms a hydrogen bond with Thr-498. Overall, our data suggest that acylation is initiated by conformational changes elicited or trapped by binding of ESCs and that these movements are restricted by mutations associated with resistance against ESCs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phonon-induced rotation of the electronic nematic director in superconducting Bi 2 Se 3

The doped topological insulator A x Bi 2 Se 3 , with A = {Cu,Sr,Nb}, becomes a nematic superconductor below T c ≈ 3–4 K. The associated electronic nematic director is described by an angle α and is experimentally manifested in the elliptical shape of the in-plane critical magnetic field H c2 . Because of the threefold rotational symmetry of the lattice, α is expected to align with one of three high-symmetry directions corresponding to the in-plane nearest-neighbor bonds, consistent with a Z 3 -Potts nematic transition. Here, we show that the nematic coupling to the acoustic phonons, which makes the nematic correlation length tend to diverge along certain directions only, can fundamentally alter this phenomenology in trigonal lattices. Compared to hexagonal lattices, the former possesses a sixth independent elastic constant c14 due to the fact that the in-plane shear strain doublet (ε xx – ε yy , – 2ε xy ) and the out-of-plane shear strain doublet (2ε yz , – 2ε zx ) transform as the same irreducible representation. We find that, when c 14 overcomes a threshold value, which is expected to be the case in doped Bi 2 Se 3 , the nematic director α unlocks from the high-symmetry directions due to the competition between the quadratic phonon-mediated interaction and the cubic nematic anharmonicity. This implies the breaking of the residual in-plane twofold rotational symmetry (C 2x ), resulting in a triclinic phase. Furthermore, we discuss the implications of these findings for the structure of nematic domains, for the shape of the in-plane H c2 in A x Bi 2 Se 3 , and for the presence of nodes inside the superconducting state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Hysteretic magnetoresistance and unconventional anomalous Hall effect in the frustrated magnet TmB 4

We study TmB 4 , a frustrated magnet on the Archimedean Shastry-Sutherland lattice, through magnetization and transport experiments. The lack of anisotropy in resistivity shows that TmB4 is an electronically three-dimensional system. The magnetoresistance (MR) is hysteretic at low temperature even though a corresponding hysteresis in magnetization is absent. The Hall resistivity shows unconventional anomalous Hall effect (AHE) and is linear above saturation despite a large MR. In conclusion, we propose that complex structures at magnetic domain walls may be responsible for the hysteretic MR and may also lead to the AHE.

36 MATERIALS SCIENCE↗

Learnability Transitions in Monitored Quantum Dynamics via Eavesdropper’s Classical Shadows

Monitored quantum dynamics—unitary evolution interspersed with measurements—has recently emerged as a rich domain for phase structure in quantum many-body systems away from equilibrium. Here we study monitored dynamics from the point of view of an eavesdropper who has access to the classical measurement outcomes, but not to the quantum many-body system. We show that a measure of information flow from the quantum system to the classical measurement record—the —undergoes a phase transition in correspondence with the measurement-induced phase transition (MIPT). This transition determines the eavesdropper’s (in)ability to learn properties of an unknown initial quantum state of the system, given a complete classical description of the monitored dynamics and arbitrary classical computational resources. We make this learnability transition concrete by defining classical shadow protocols that the eavesdropper may apply to this problem, and show that the MIPT manifests as a transition in the sample complexity of various shadow-estimation tasks, which become harder in the low-measurement phase. We focus on three applications of interest: Pauli expectation values (where we find the MIPT appears as a point of optimal learnability for typical Pauli operators), many-body fidelity, and global charge in U ( 1 ) -symmetric dynamics. Our work unifies different manifestations of the MIPT under the umbrella of and gives this notion a general operational meaning via classical shadows. Published by the American Physical Society 2024

Physics↗

Imaging orbital ferromagnetism in a moiré Chern insulator

Capturing exotic magnetism Ferromagnetism is associated with the breaking of time-reversal symmetry, most frequently by the spin degree of freedom. Although the orbital motion of electrons can also contribute to ferromagnetism, in most materials, it is small relative to the spin contribution. Tschirhart et al. showed that the reverse is true in an unusual magnetic state hosted by twisted bilayer graphene. Their scanning magnetometry measurements were consistent with ferromagnetism of predominantly orbital origin. Science , abd3190, this issue p. 1323

Science & Technology - Other Topics↗

Small-angle scattering study of Aspergillus awamori glycoprotein glucoamylase

Glucoamylase from fungus Aspergillus awamori is glycoside hydrolase that catalyzes the hydrolysis of α-1,4- and α-1,6-glucosidic bonds in glucose polymers and oligomers. This glycoprotein consists of a catalytic domain and a starch-binding domain connected by an O-glycosylated polypeptide chain. The conformation of the linker, the relative arrangement of the domains, and the structure of the full-length enzyme are unknown. The structure of the recombinant glucoamylase GA1 was studied by molecular modelling and small-angle neutron scattering (SANS) methods. The experimental SANS data provide evidence that glucoamylase exists as a monomer in solution and contains a glycoside component, which makes a substantial contribution to the scattering. The model of full-length glucoamylase, which was calculated without taking into account the effect of glycosylation, is consistent with the experimental data and has a radius of gyration of 33.4 ± 0.6 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PolyID™ (Polymer Inverse Design) [SWR-21-98]

PolyID™ provides a framework for building, training, and predicting polymer properties using graph neural networks. The codes leverages Neural Fingerprint (nfp) (See DOE Code ID 22185) for building tensorflow-based message-passing neural networks, and Monomers to Polymers (m2p) (See DOE Code ID 44795) for building polymer structures. To understand and use the pipeline, the following examples have been provided: Building polymer structures: examples/example_generate_polymer_structures.ipynb Checking domain of validity: examples/example_determine_domain-of-validity.ipynb Training a graph neural network: examples/example_generate_and_train_models.ipynb Predicting with the trained model: examples/example_predict_with_trained_models.ipynb

Wilson, Nolan↗

Multimodal Atomic Force Microscopy for the Characterization of Metallic Particulates

This study investigates the utility of multimodal, or functional, atomic force microscopy (AFM) for the characterization of individual particles and particle ensembles. In single-particle analyses, AFM imaging modes provided orthogonal insights into mechanical and magnetic properties that are not accessible through conventional electron microscopy. Although the experiments were inherently delicate and time-intensive, with an observed sample loss rate of approximately 30%, these techniques enabled the qualitative differentiation of grain structures and magnetic domains, underscoring the challenges of experimental robustness. For particle ensembles, AFM enabled the extraction of reliable 2D and 3D particle size distributions. However, efforts to chemically differentiate particles based on mechanical property contrasts were limited by scaling effects and the qualitative nature of the data. Overall, multimodal AFM offers valuable complementary information, but its application requires careful consideration of methodological limitations, particularly for sample integrity, calibration, and scalability of mechanical and magnetic measurements. This report is organized to first address the application of AFM to single-particle analysis using various imaging modalities, followed by its potential role in ensemble-level particle screening and differentiation.

36 MATERIALS SCIENCE↗

Processing of laser formed SiC powder

Superior SiC characteristics can be achieved through the use of ideal constituent powders and careful post-synthesis processing steps. High purity SiC powders of approx. 1000 A uniform diameter, nonagglomerated and spherical were produced. This required major revision of the particle formation and growth model from one based on classical nucleation and growth to one based on collision and coalescence of Si particles followed by their carburization. Dispersions based on pure organic solvents as well as steric stabilization were investigated. Although stable dispersions were formed by both, subsequent part fabrication emphasized the pure solvents since fewer problems with drying and residuals of the high purity particles were anticipated. Test parts were made by the colloidal pressing technique; both liquid filtration and consolidation (rearrangement) stages were modeled. Green densities corresponding to a random close packed structure (approx. 63%) were achieved; this highly perfect structure has a high, uniform coordination number (greater than 11) approaching the quality of an ordered structure without introducing domain boundary effects. After drying, parts were densified at temperatures ranging from 1800 to 2100 C. Optimum densification temperatures will probably be in the 1900 to 2000 C range based on these preliminary results which showed that 2050 C samples had experienced substantial grain growth. Although overfired, the 2050 C samples exhibited excellent mechanical properties. Biaxial tensile strengths up to 714 MPa and Vickers hardness values of 2430 kg/sq mm 2 were both more typical of hot pressed than sintered SiC. Both result from the absence of large defects and the confinement of residual porosity (less than 2.5%) to small diameter, uniformly distributed pores.

Haggerty, J. S.↗

Design sensitivity analysis using EAL. Part 2: Shape design parameters

A numerical implementation of shape design sensitivity analysis of built-up structures is presented, using the versatility and convenience of an existing finite element structural analysis code and its data base management system. This report is a continuation of a previous report on conventional design parameters. The finite element code used in the implementation presented is the Engineering Analysis Language (EAL), which is based on a hybrid analysis method. It has been shown that shape design sensitivity computations can be carried out using the database management system of EAL, without writing a separate program and a separate data base. The material derivative concept of continuum mechanics and an adjoint variable method of design sensitivity analysis are used to derive shape design sensitivity information of structural performances. A domain method of shape design sensitivity analysis and a design component method are used. Displacement and stress functionals are considered as performance criteria.

Dopker, B.↗

Distributed deformation and block rotation in 3D

The authors address how block rotation and complex distributed deformation in the Earth's shallow crust may be explained within a stationary regional stress field. Distributed deformation is characterized by domains of sub-parallel fault-bounded blocks. In response to the contemporaneous activity of neighboring domains some domains rotate, as suggested by both structural and paleomagnetic evidence. Rotations within domains are achieved through the contemporaneous slip and rotation of the faults and of the blocks they bound. Thus, in regions of distributed deformation, faults must remain active in spite of their poor orientation in the stress field. The authors developed a model that tracks the orientation of blocks and their bounding faults during rotation in a 3D stress field. In the model, the effective stress magnitudes of the principal stresses (sigma sub 1, sigma sub 2, and sigma sub 3) are controlled by the orientation of fault sets in each domain. Therefore, adjacent fault sets with differing orientations may be active and may display differing faulting styles, and a given set of faults may change its style of motion as it rotates within a stationary stress regime. The style of faulting predicted by the model depends on a dimensionless parameter phi = (sigma sub 2 - sigma sub 3)/(sigma sub 1 - sigma sub 3). Thus, the authors present a model for complex distributed deformation and complex offset history requiring neither geographical nor temporal changes in the stress regime. They apply the model to the Western Transverse Range domain of southern California. There, it is mechanically feasible for blocks and faults to have experienced up to 75 degrees of clockwise rotation in a phi = 0.1 strike-slip stress regime. The results of the model suggest that this domain may first have accommodated deformation along preexisting NNE-SSW faults, reactivated as normal faults. After rotation, these same faults became strike-slip in nature.

Scotti, Oona↗

Finite element solution of transient fluid-structure interaction problems

A finite element approach using NASTRAN is developed for solving time-dependent fluid-structure interaction problems, with emphasis on the transient scattering of acoustic waves from submerged elastic structures. Finite elements are used for modeling both structure and fluid domains to facilitate the graphical display of the wave motion through both media. For the liquid, the use of velocity potential as the fundamental unknown results in a symmetric matrix equation. The approach is illustrated for the problem of transient scattering from a submerged elastic spherical shell subjected to an incident tone burst. The use of an analogy between the equations of elasticity and the wave equation of acoustics, a necessary ingredient to the procedure, is summarized.

Everstine, Gordon C.↗

Integrated Vertical Bloch Line (VBL) memory

Vertical Bloch Line (VBL) Memory is a recently conceived, integrated, solid state, block access, VLSI memory which offers the potential of 1 Gbit/sq cm areal storage density, data rates of hundreds of megabits/sec, and submillisecond average access time simultaneously at relatively low mass, volume, and power values when compared to alternative technologies. VBLs are micromagnetic structures within magnetic domain walls which can be manipulated using magnetic fields from integrated conductors. The presence or absence of BVL pairs are used to store binary information. At present, efforts are being directed at developing a single chip memory using 25 Mbit/sq cm technology in magnetic garnet material which integrates, at a single operating point, the writing, storage, reading, and amplification functions needed in a memory. The current design architecture, functional elements, and supercomputer simulation results are described which are used to assist the design process.

Katti, R. R.↗

Multidisciplinary aeroelastic analysis of a generic hypersonic vehicle

This paper presents details of a flutter and stability analysis of aerospace structures such as hypersonic vehicles. Both structural and aerodynamic domains are discretized by the common finite element technique. A vibration analysis is first performed by the STARS code employing a block Lanczos solution scheme. This is followed by the generation of a linear aerodynamic grid for subsequent linear flutter analysis within subsonic and supersonic regimes of the flight envelope; the doublet lattice and constant pressure techniques are employed to generate the unsteady aerodynamic forces. Flutter analysis is then performed for several representative flight points. The nonlinear flutter solution is effected by first implementing a CFD solution of the entire vehicle. Thus, a 3-D unstructured grid for the entire flow domain is generated by a moving front technique. A finite element Euler solution is then implemented employing a quasi-implicit as well as an explicit solution scheme. A novel multidisciplinary analysis is next effected that employs modal and aerodynamic data to yield aerodynamic damping characteristics. Such analyses are performed for a number of flight points to yield a large set of pertinent data that define flight flutter characteristics of the vehicle. This paper outlines the finite-element-based integrated analysis procedures in detail, which is followed by the results of numerical analyses of flight flutter simulation.

Gupta, K. K.↗

Non-local sub-characteristic zones of influence in unsteady interactive boundary-layers

The properties of incompressible, unsteady, interactive, boundary layers are examined for a model hypersonic boundary layer and internal flow past humps or, equivalently, external flow past short-scaled humps. Using a linear high frequency analysis, it is shown that the domains of dependence within the viscous sublayer may be a strong function of position within the sublayer and may be strongly influenced by the pressure displacement interaction, or the prescribed displacement condition. Detailed calculations are presented for the hypersonic boundary layer. This effect is found to carry over directly to the fully viscous problem as well as the nonlinear problem. In the fully viscous problem, the non-local character of the domains of dependence manifests itself in the sub-characteristics. Potential implications of the domain of dependence structure on finite difference computations of unsteady boundary layers are briefly discussed.

Rothmayer, A. P.↗

Eigensystem realization algorithm user's guide forVAX/VMS computers: Version 931216

The eigensystem realization algorithm (ERA) is a multiple-input, multiple-output, time domain technique for structural modal identification and minimum-order system realization. Modal identification is the process of calculating structural eigenvalues and eigenvectors (natural vibration frequencies, damping, mode shapes, and modal masses) from experimental data. System realization is the process of constructing state-space dynamic models for modern control design. This user's guide documents VAX/VMS-based FORTRAN software developed by the author since 1984 in conjunction with many applications. It consists of a main ERA program and 66 pre- and post-processors. The software provides complete modal identification capabilities and most system realization capabilities.

Pappa, Richard S.↗

Executing CLIPS expert systems in a distributed environment

This paper describes a framework for running cooperating agents in a distributed environment to support the Intelligent Computer Aided Design System (ICADS), a project in progress at the CAD Research Unit of the Design Institute at the California Polytechnic State University. Currently, the systems aids an architectural designer in creating a floor plan that satisfies some general architectural constraints and project specific requirements. At the core of ICADS is the Blackboard Control System. Connected to the blackboard are any number of domain experts called Intelligent Design Tools (IDT). The Blackboard Control System monitors the evolving design as it is being drawn and helps resolve conflicts from the domain experts. The user serves as a partner in this system by manipulating the floor plan in the CAD system and validating recommendations made by the domain experts. The primary components of the Blackboard Control System are two expert systems executed by a modified CLIPS shell. The first is the Message Handler. The second is the Conflict Resolver. The Conflict Resolver synthesizes the suggestions made by the domain experts, which can be either CLIPS expert systems, or compiled C programs. In DEMO1, the current ICADS prototype, the CLIPS domain expert systems are Acoustics, Lighting, Structural, and Thermal; the compiled C domain experts are the CAD system and the User Interface.

Taylor, James↗