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At least 667 records · Page 37

A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes

Abstract Complement evasion is a hallmark of extracellular microbial pathogens such as Borrelia burgdorferi, the causative agent of Lyme disease. Lyme disease spirochetes express nearly a dozen outer surface lipoproteins that bind complement components and interfere with their native activities. Among these, BBK32 is unique in its selective inhibition of the classical pathway. BBK32 blocks activation of this pathway by selectively binding and inhibiting the C1r serine protease of the first component of complement, C1. To understand the structural basis for BBK32-mediated C1r inhibition, we performed crystallography and size-exclusion chromatography–coupled small angle X-ray scattering experiments, which revealed a molecular model of BBK32-C in complex with activated human C1r. Structure-guided site-directed mutagenesis was combined with surface plasmon resonance binding experiments and assays of complement function to validate the predicted molecular interface. Analysis of the structures shows that BBK32 inhibits activated forms of C1r by occluding substrate interaction subsites (i.e., S1 and S1’) and reveals a surprising role for C1r B loop–interacting residues for full inhibitory activity of BBK32. The studies reported in this article provide for the first time (to our knowledge) a structural basis for classical pathway–specific inhibition by a human pathogen.

Garrigues, Ryan J. (ORCID:0000000259233250)↗

An expert system shell for inferring vegetation characteristics: Interface for the addition of techniques (Task H)

All the NASA VEGetation Workbench (VEG) goals except the Learning System provide the scientist with several different techniques. When VEG is run, rules assist the scientist in selecting the best of the available techniques to apply to the sample of cover type data being studied. The techniques are stored in the VEG knowledge base. The design and implementation of an interface that allows the scientist to add new techniques to VEG without assistance from the developer were completed. A new interface that enables the scientist to add techniques to VEG without assistance from the developer was designed and implemented. This interface does not require the scientist to have a thorough knowledge of Knowledge Engineering Environment (KEE) by Intellicorp or a detailed knowledge of the structure of VEG. The interface prompts the scientist to enter the required information about the new technique. It prompts the scientist to enter the required Common Lisp functions for executing the technique and the left hand side of the rule that causes the technique to be selected. A template for each function and rule and detailed instructions about the arguments of the functions, the values they should return, and the format of the rule are displayed. Checks are made to ensure that the required data were entered, the functions compiled correctly, and the rule parsed correctly before the new technique is stored. The additional techniques are stored separately from the VEG knowledge base. When the VEG knowledge base is loaded, the additional techniques are not normally loaded. The interface allows the scientist the option of adding all the previously defined new techniques before running VEG. When the techniques are added, the required units to store the additional techniques are created automatically in the correct places in the VEG knowledge base. The methods file containing the functions required by the additional techniques is loaded. New rule units are created to store the new rules. The interface that allow the scientist to select which techniques to use is updated automatically to include the new techniques. Task H was completed. The interface that allows the scientist to add techniques to VEG was implemented and comprehensively tested. The Common Lisp code for the Add Techniques system is listed in Appendix A.

Harrison, P. Ann↗

Interfacial Inversion of Stealth Surfactants

Amphiphilic macromolecular surfactants segregate to liquid–liquid interfaces, thereby reducing the interfacial tension and free energy. Here, we investigated “stealth surfactants” in the form of core–shell bottlebrush polymers comprised of pH-responsive diblock copolymer side chains forming a hydrophilic core and a hydrophobic shell, enabling solubility in oil. At liquid–liquid interfaces, these polymers undergo a structural “inversion”, with hydrophilic blocks segregating into the aqueous phase and hydrophobic blocks residing in the oil phase. The reconfiguration kinetics and surfactant properties are influenced by multiple factors, including the molecular weights of the backbone and side chain components, the hydrophilic-to-hydrophobic balance of the side chains, and the pH of the aqueous phase. An observed nonmonotonic dependence of interfacial tension with time is attributed to a progressive structural inversion, where the projected area of the macromolecule onto the interface decreases. To validate this inversion hypothesis, interfacial properties were characterized by sum-frequency generation vibrational spectroscopy, which revealed configurational changes of the core–shell bottlebrush polymers at the fluid interface and revealed a pH-dependent interfacial coverage. Coarse-grained molecular dynamics simulations supported these experimental findings, showing that the pH-responsive core and hydrophobic shell assume a time-averaged configuration with orientations parallel and perpendicular to the plane of the interface, respectively. These findings open routes to design multistimuli-responsive polymeric surfactants and compatibilizers, expanding their potential applications in advanced interfacial systems.

Stealth surfactants↗

Space Shuttle Orbiter AFT heat shield seal

The evolution of the orbiter aft heat shield seal (AHSS) design, which involved advancing mechanical seal technology in severe thermal environment is discussed. The baseline design, various improvements for engine access, and technical problem solution are presented. It is a structure and mechanism at the three main propulsion system (MPS) engine interfaces to the aft compartment structure. Access to each MPS engine requires disassembly and removal of the AHSS. Each AHSS accommodates the engine movement, is exposed to an extremely high temperature environment, and is part of the venting control of the aft compartment.

Walkover, L. J.↗

Generalized pulse equations for through-transmission evaluation of arbitrary multilayered structures

Generalized transit time and pulse amplitude equations were derived for modelling the ultrasonic through-transmission wave propagation of an arbitrary n-layered structure. The equations can be programmed into an expert system and used to identify and predict the through-transmission pulse signals from the critical interfaces of a multilayered structure. To test the formulas, the through transmission was measured from one- and three-layered configurations in the laboratory. The experimental measurements were compared with computer-generated data determined using the derived equations. The results verify the validity of the formulas.

Chern, E. James↗

Generalized pulse equations for through-transmission evaluation of arbitrary multilayered structures

Generalized transit-time and pulse-amplitude equations have been derived for modeling the ultrasonic through-transmission wave propagation of an arbitrary n-layered structure. The equations can be programmed into an expert system and used to identify and predict the through-transmission pulse signals from the critical interfaces of a multilayered structure. To test the formulas, the through-transmission responses from one- and three-layered configurations were measured in the laboratory and compared with computer-generated data that were determined using the derived equations. The results verify the validity of the formulas.

Chern, E. James↗

Novel Microstructures for Polymer-Liquid Crystal Composite Materials

There are a number of interface-dominated composite materials that contain a liquid crystalline (LC) phase in intimate contact with an isotropic phase. For example, polymer- dispersed liquid crystals, used in the fabrication of windows with switchable transparency, consist of micron size LC droplets dispersed in an isotropic polymer matrix. Many other types of liquid crystal composite materials can be envisioned that might have outstanding optical properties that could be exploited in novel chemical sensors, optical switches, and computer displays. This research project was based on the premise that many of these potentially useful LC composite materials can only be fabricated under microgravity conditions where gravity driven flows are absent. In the ground-based research described below, we have focused on a new class of LC composites that we call thermotropic- lyotropic liquid crystal systems (TLLCs). TLLCs consist of nanosize droplets of water dispersed in an LC matrix, with surfactants at the interface that stabilize the structure. By varying the type of surfactant one can access almost an infinite variety of unusual LC composite microstructures. Due to the importance of the interface in these types of systems, we have also developed molecular simulation models for liquid crystals at interfaces, and made some of the first measurements of the interfacial tension between liquid crystals and water.

Magda, Jules J.↗

Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G

APOBEC3G, a member of the double-domain cytidine deaminase (CD) APOBEC, binds RNA to package into virions and restrict HIV-1 through deamination-dependent or deamination-independent inhibition. Mainly due to lack of a full-length double-domain APOBEC structure, it is unknown how CD1/CD2 domains connect and how dimerization/multimerization is linked to RNA binding and virion packaging for HIV-1 restriction. We report rhesus macaque A3G structures that show different inter-domain packing through a short linker and refolding of CD2. The A3G dimer structure has a hydrophobic dimer-interface matching with that of the previously reported CD1 structure. A3G dimerization generates a surface with intensified positive electrostatic potentials (PEP) for RNA binding and dimer stabilization. Unexpectedly, mutating the PEP surface and the hydrophobic interface of A3G does not abolish virion packaging and HIV-1 restriction. The data support a model in which only one RNA-binding mode is critical for virion packaging and restriction of HIV-1 by A3G.

59 BASIC BIOLOGICAL SCIENCES↗

Advanced Computational Modeling Approaches for Shock Response Prediction

Motivation: (1) The activation of pyroshock devices such as explosives, separation nuts, pin-pullers, etc. produces high frequency transient structural response, typically from few tens of Hz to several hundreds of kHz. (2) Lack of reliable analytical tools makes the prediction of appropriate design and qualification test levels a challenge. (3) In the past few decades, several attempts have been made to develop methodologies that predict the structural responses to shock environments. (4) Currently, there is no validated approach that is viable to predict shock environments overt the full frequency range (i.e., ~100 Hz to 10 kHz). Scope: (1) Model, analyze, and interpret space structural systems with complex interfaces and discontinuities, subjected to shock loads. (2) Assess the viability of a suite of numerical tools to simulate transient, non-linear solid mechanics and structural dynamics problems, such as shock wave propagation.

Derkevorkian, Armen↗

Structural zooming research and development of an interactive computer graphical interface for stress analysis of cracks

Engineering problems sometimes involve the numerical solution of boundary value problems over domains containing geometric feature with widely varying scales. Often, a detailed solution is required at one or more of these features. Small details in large structures may have profound effects upon global performance. Conversely, large-scale conditions may effect local performance. Many man-hours and CPU-hours are currently spent in modeling such problems. With the structural zooming technique, it is now possible to design an integrated program which allows the analyst to interactively focus upon a small region of interest, to modify the local geometry, and then to obtain highly accurate responses in that region which reflect both the properties of the overall structure and the local detail. A boundary integral equation analysis program, called BOAST, was recently developed for the stress analysis of cracks. This program can accurately analyze two-dimensional linear elastic fracture mechanics problems with far less computational effort than existing finite element codes. An interactive computer graphical interface to BOAST was written. The graphical interface would have several requirements: it would be menu-driven, with mouse input; all aspects of input would be entered graphically; the results of a BOAST analysis would be displayed pictorially but also the user would be able to probe interactively to get numerical values of displacement and stress at desired locations within the analysis domain; the entire procedure would be integrated into a single, easy to use package; and it would be written using calls to the graphic package called HOOPS. The program is nearing completion. All of the preprocessing features are working satisfactorily and were debugged. The postprocessing features are under development, and rudimentary postprocessing should be available by the end of the summer. The program was developed and run on a VAX workstation, and must be ported to the SUN workstation. This activity is currently underway.

Gerstle, Walter↗

Time-Resolved Structural Measurement of Thermal Resistance across a Buried Semiconductor Heterostructure Interface

The precise control and understanding of heat flow in heterostructures is pivotal for advancements in thermoelectric energy conversion, thermal barrier coatings, and efficient heat management in electronic and optoelectronic devices. In this study, we employ high-angular-resolution time-resolved X-ray diffraction to structurally measure thermal resistance in a laser-excited AlGaAs/GaAs semiconductor heterostructure. Our methodology offers femtometer-scale spatial sensitivity and nanosecond time resolution, enabling us to directly observe heat transport across a buried interface. We corroborate established Thermal Boundary Resistance (TBR) values for AlGaAs/GaAs heterostructures and demonstrate that TBR arises from material property discrepancies on either side of a nearly flawless atomic interface. This work not only sheds light on the fundamental mechanisms governing heat flow across buried interfaces but also presents a robust experimental framework that can be extended to other heterostructure systems, paving the way for optimized thermal management in next-generation devices.

36 MATERIALS SCIENCE↗

ISO_Fortran_binding_m v0.1.0

The Fortran programming language standard defines a broad feature set supporting the interoperability of Fortran programs with program written according to the C programming language standard. Among Fortran's C-interoperability features is a a C header file "ISO_Fortran_binding.h" This header file defines the interface to various C data structures and functions that C programs may use to access Fortran data entities. The ISO_Fortran_binding_m software defines a native Fortran module that presents an interface to these same data structures and functions. ISO_Fortran_bind_m thus enables Fortran programs to access and manipulate Fortran entities in ways that precisely mirror what C programs can do using ISO_Fortran_binding.h. ISO_Fortran_binding_m facilitates writing portable standard-conforming Fortran programs that emulate non-interoperable features, e.g., dynamic polymorphism, in a standard-conforming interoperable way similar but broader than what is demonstrated in Berkeley Lab's Caffeine software [1]. ISO_Fortran_binding_m also enables a Fortran programmer to extend Fortran's capabilities to emulate certain C functionality such as memory address arithmetic or computing C's "sizeof" function. [1] https://github.com/BerkeleyLab/caffeine/blob/213e3df1c319f0663306354414f352acda42a24f/src/caffeine/collective_subroutines/co_reduce_s.f90#L88 [2] https://github.com/BerkeleyLab/ISO_Fortran_binding_m/blob/0c585362bb4f2c72cf9049c800a7115b529ec533/src/iso_fortran_binding_m.F90#L196

Rouson, Damian↗

Effect of Salt Concentration on the Interfacial Solvation Structure and Early Stage of Solid–Electrolyte Interphase Formation in Ca(BH 4 ) 2 /THF for Ca Batteries

The Ca 2+ solvation structure at the electrolyte/electrode interface is of central importance to understand electroreduction stability and solid–electrolyte interphase (SEI) formation for the novel multivalent Ca battery systems. Here, using an exemplar electrolyte, the concentration-dependent solvation structure of Ca(BH 4 ) 2 -tetrahydrofuran on a gold model electrode has been investigated with various electrolyte concentrations via electrochemical quartz crystal microbalance with dissipation (EQCM-D) and X-ray photoelectron spectroscopy (XPS). For the first time, in situ EQCM-D results prove that the prevalent species adsorbed at the interface is CaBH 4 + across all concentrations. As the salt concentration increases, the number of BH 4 – anions associated with Ca 2+ increases, and much larger solvated complexes such as CaBH 4 + ·4THF or Ca(BH 4 ) 3 – ·4THF form at the interface at high concentrations prior to Ca plating. Different interfacial chemistries lead to the formation of SEIs with different components demonstrated by XPS. High electrolyte concentrations reduce the solvent decomposition and promote the formation of thick, uniform, and inorganic-rich (i.e., CaO) SEI layers, which contribute to improved Ca plating efficiency and current density in electrochemical measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Low energy dislocation structures in epitaxy

The principle of minimum energy was applied to epitaxial interfaces to show the interrelationship beteen misfit, overgrowth thickness and misfit dislocation spacing. The low energy dislocation configurations were presented for selected interfacial geometries. A review of the interfacial energy calculations was made and a critical assessment of the agreement between theory and experiment was presented. Modes of misfit accommodation were presented with emphasis on the distinction between kinetic effects and equilibrium conditions. Two-dimensional and three-dimensional overgrowths were treated together with interdiffusion-modified interfaces, and several models of interfacial structure were treated including the classical and the current models. The paper is concluded by indicating areas of needed investigation into interfacial structure.

Van Der Merwe, Jan H.↗

An introduction to the Gilgamesh PIM architecture

The focus of the work conducted is on a class of structures made possible by the merger of logic and memory. Processing In Memory (PIM) extends the design space much farther by closely associating the logic with the memory interface to realize innovative structures never previously possible and thus exposing entirely new opportunities for computer architecture.

Gilgamesh PIM CMOS↗

A robust interface finite element formulation for modeling brittle material failure problems

Abstract Failure of many brittle materials and structures can be modeled using interface‐oriented finite elements combined with intrinsic cohesive zone models. The discontinuous Galerkin (DG) finite element method provides an innovative framework for modeling brittle crack propagation with zero‐thickness interface elements, which can accommodate extrinsic cohesive laws to avoid the artificial compliance required in intrinsic cohesive models. However, robust formulations and implementations of DG methods are critical in alleviating the well‐known convergence issues for both crack nucleation and propagation with reduced instability. This paper presents a robust interface element formulation by modifying the incomplete interior penalty Galerkin (IIPG) method, which successfully avoids the initial element interface penetration across elements that occurs prior to crack nucleation, and thereby greatly reduces the instability issue as cracks open. We further verified and validated our implementation by using a bar tension test and a beam fracturing benchmark. The robustness of our proposed interface element method was demonstrated by a micromechanics fiber/matrix debonding problem with 64 fibers embedded in a bulk matrix.

Liu, Ruijie↗

Natural formation of linear defect structures in MoS 2

Near surface defects can significantly impact the quality of metallic interconnects and other interfaces necessary to create device structures incorporating two-dimensional materials. Furthermore, the impact of such defects can strongly depend on their organization. In this study, we present scanning tunneling microscopy images and tunneling spectroscopy of point and linear defects near the surface of natural MoS 2 . The point defects share similar structural and electronic characteristics and occur with comparable frequency as subsurface sulfur vacancies observed previously on natural MoS 2 . The linear defects observed here occur less frequently than the point defects but share the same depth profile and electronic structure. These data indicate that the linear defects are actually a one-dimensional organization of subsurface sulfur vacancies. Our density functional calculations agree with this assessment in that, for sufficient local defect concentrations, it is energetically more favorable for the defects to be organized in a linear fashion rather than as clusters or even isolated single point defects. Given these measurements were taken from naturally formed MoS 2 , this organization likely occurs during crystal formation. Considering the impact of one-dimensional organization on the local properties of layered materials, and the potential for them to be introduced purposefully during crystal formation, research into the formation mechanism and properties of these defects could enable new paths for defect engineering in MoS 2 -based systems.

2D materials↗