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At least 487 records · Page 27

Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of Chlamydia and may better inform rational vaccine design and functional studies.

59 BASIC BIOLOGICAL SCIENCES↗

Realization of high quality production schedules: Structuring quality factors via iteration of user specification processes

This paper describes an architecture for realizing high quality production schedules. Although quality is one of the most important aspects of production scheduling, it is difficult, even for a user, to specify precisely. However, it is also true that the decision as to whether a scheduler is good or bad can only be made by the user. This paper proposes the following: (1) the quality of a schedule can be represented in the form of quality factors, i.e. constraints and objectives of the domain, and their structure; (2) quality factors and their structure can be used for decision making at local decision points during the scheduling process; and (3) that they can be defined via iteration of user specification processes.

Hamazaki, Takashi↗

The carboxylation status of osteocalcin has important consequences for its structure and dynamics

The carboxylation status of Osteocalcin (Ocn) not only influences formation and structure in bones but also has important endocrine functions affecting energy metabolism and expenditure. In this study, the role of γ-carboxylation of the glutamate residues in the structure-dynamics-function relationship in Ocn is investigated. Three forms of Ocn, differentially carboxylated at the Glu-17, 21 and 24 residues, along with a mutated form of Ocn carrying Glu/Ala mutations, are modeled and simulated using molecular dynamics (MD) simulation in the presence of calcium ions. Characterization of the global conformational dynamics of Ocn, described in terms of the orientational variations within its 3-helical domain, highlights large structural variations in the non-carboxylated osteocalcin (nOcn). The bi-carboxylated Ocn (bOcn) and tri-carboxylated (tOcn) species, in contrast, display relatively rigid tertiary structures, with the dynamics of most regions strongly correlated. Radial distribution functions calculated for both bOcn and tOcn show long-range ordering of the calcium ion distribution around the carboxylated glutamate (γGlu) residues, likely playing an important role in promoting stability of these Ocns. Additionally, the same calcium ions are observed to coordinate with neighboring γGlu, better shielding their negative charges and in turn stabilizing these systems more than do the singly coordinating calcium ions observed in the case of nOcn. bOcn is also found to exhibit a more helical C-terminal structure, that has been shown to activate its cellular receptor GPRC6A, highlighting the allosteric role of Ocn carboxylation in modulating the stability and binding potential of the active C-terminal. Furthermore, the carboxylation status of Ocn as well and its calcium coordination appear to have a direct influence on Ocn structure and dynamics, possibly leading to the known differences in Ocn biological function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Generalized Symbolic Execution for Model Checking and Testing

Modern software systems, which often are concurrent and manipulate complex data structures must be extremely reliable. We present a novel framework based on symbolic execution, for automated checking of such systems. We provide a two-fold generalization of traditional symbolic execution based approaches: one, we define a program instrumentation, which enables standard model checkers to perform symbolic execution; two, we give a novel symbolic execution algorithm that handles dynamically allocated structures (e.g., lists and trees), method preconditions (e.g., acyclicity of lists), data (e.g., integers and strings) and concurrency. The program instrumentation enables a model checker to automatically explore program heap configurations (using a systematic treatment of aliasing) and manipulate logical formulae on program data values (using a decision procedure). We illustrate two applications of our framework: checking correctness of multi-threaded programs that take inputs from unbounded domains with complex structure and generation of non-isomorphic test inputs that satisfy a testing criterion. Our implementation for Java uses the Java PathFinder model checker.

Khurshid, Sarfraz↗

Antiphase-Boundary-Engineered Domain Switching in a (110)-Oriented BiFeO 3 Film

A ferroelectric domain wall memory device exploits the presence (or absence) of domain walls as the basis for information storage. Although structural defects strongly influence ferroelectric domain wall nucleation and growth, this correlation is far from being fully understood. For example, a single defect can play opposing roles: it can act as a nucleation site to initiate domain switching or, conversely, serve as a pinning center inhibiting domain wall motion. This is particularly the case for antiphase boundaries (APBs), whose influence on switching remains relatively unexplored despite being ubiquitous in oxide perovskite ferroelectrics. Here, we use aberration-corrected scanning transmission microscopy and in situ transmission electron microscopy under an applied bias to extensively characterize the influence of an APB on the switching behavior in a (110)-oriented BiFeO 3 thin film. We demonstrate that deterministic nucleation occurs in the proximity of a vertically oriented APB, following which domain growth occurs laterally in a symmetric fashion. Atomic-scale structural analysis reveals that the shear operation vector for the APB is 1/2[110]; this half-unit-cell shift extends over a few nanometers, implying that the APB plane is inclined toward the imaging direction. The symmetric switching observation is attributed to local inhomogeneous lattice strain and a reduction of polarization caused by the APB. These results demonstrate that an extended structural defect can be used as an active switching element rather than a stumbling block in reprogrammable domain-wall-based devices. Ultimately, this will expand the capabilities of ferroelectric thin films for future electronic devices based on ferroelectric domain walls.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Physical state of the western U.S. upper mantle

Using observed P wave images of the western U.S. upper mantle, which show lateral variations of up to 8%, and existing scaling relations, we infer that the low-velocity mantle is hot and partially molten to depths of 100-200 km, and that the high-velocity upper mantle is subsolidus. Most the high-velocity upper mantle within a few hundred kilometers of the coastline appears to be relatively dense, suggesting that it is relatively cool (i.e., a thermal lithosphere). This is expected for features associated with the subducting Juan de Fuca and Gorda slabs, and the high velocity upper mantle beneath the Transverse Ranges has been attributed to the sinking of negatively buoyant mantle lithosphere. Other high-velocity mantle structures near the continental margin are consistent with this interpretation. In contrast, the generally high elevations of the continental interior imply a buoyant upper mantle there, an inference that holds for both the high- and the low-velocity upper mantle. The only resonable way to produce the high-velocity low-density upper mantle is through basalt depletion, thereby creating mantle of increased solidus temperature and decreased density. We distinguish a marginal domain, within approximately 250 km of the Pacific coast, from an interior domain. This is based on the inferred upper mantle compositional difference and regional associations: beneath the marginal domain, upper mantle structures trend parallel to the surface physiography and young tectonic structures, whereas upper mantle structures beneath the continental interior trend northeasterly. This northeast orientation is discordant with the young tectonic structures, but aligns with young volcanic activity. The high lateral gradients in observed upper mantle seismic structure found throughout the western United States imply high lateral gradients in the associated temperature or partial melt fields. Because these fields diffuse on time scales of less than a few tens of millions of years, the imaged upper mantle structure is young. The following upper mantle processes are hypothesized to account for these findings and inferences. Away from the plate margin, small-scale upper mantle convection driven by partial melt-induced buoyancy of hot upper mantle leads to the production and segregation of melt and the creation of compositional variations. The heterogeneous upper mantle P wave structure of the elevated continental interior is largely a consequence of partial melt variations that are modulated by the compositional variations, and throughout this region we infer high temperatures and low densities. Near the plate margin, relative plate motions force upper mantle flow, although upper mantle flow driven by the positive buoyancy of melt and the negative bouyancy lithosphere is important locally.

Humphreys, Eugene D.↗

Condensation of collective polar vortex modes

The dynamics of extended objects such as domain walls, domain bubbles, vortex structures, etc., can be described by their equations of motion associated with their effective mass and spring constant. Here we analytically derive the equations of motion for the polarization dynamics and elastodynamics for the structural responses of ferroelectric polar vortices, and theoretically extract their effective mass, spring constant, and mode frequencies. We demonstrate two subterahertz phonon modes and predicted their frequencies, both consistent with our recent experimental measurements and phase-field simulations. We show that elastic modulation of the energy function and spring constants leads to a condensation of a collective mode upon a second-order structural transition from symmetric to asymmetric vortices at a critical strain, analogous to the ferroelectric soft phonon mode at a ferroelectric transition. Furthermore, the present work offers a theoretical framework for predicting and manipulating the ultrafast collective dynamics of polar nanostructures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Domain Nucleation and Growth in an Epitaxially Grown Wurtzite Ferroelectric

Ferroelectric domain nucleation and growth in epitaxial (Al, B, Sc)N films grown on n-GaN substrates are explored using a combination of ferroelectric property measurements and scanning transmission electron microscopy, including novel in situ switching studies. The films are electrically switched to nitrogen-polar (N-polar) and metal-polar (M-polar) configurations, attaining a remanent polarization of 120 µC cm −2 with coercive fields of ≈6 MV cm −1 . In the initial switching cycle, the ferroelectric domains nucleate near the bottom n-GaN electrode and develop domain walls with zigzag morphologies, while residual “dead layers” that do not switch from the as-deposited orientation persist at the top and bottom electrodes. The in situ microscopy experiments reveal that domain walls propagate fastest in the lateral direction, parallel to the electrode/film interface. These findings provide insights into the domain dynamics and structural evolution of wurtzite ferroelectrics, offering implications for next-generation electronic devices.

36 MATERIALS SCIENCE↗

Theory of strain phase equilibria and diagrams

Chemical phase equilibria and phase diagrams are well established and have served as indispensable guides for designing materials through chemical tuning. However, a general thermodynamic theory for strain phase equilibria remains elusive despite extensive studies which have revealed dramatic impacts of mechanical strain on the stability of phases and domain states in solid-state materials. Here, we establish the thermodynamic theory of strain equilibria and a general framework for efficiently constructing multidomain and multiphase diagrams of arbitrarily strained solids under incoherent conditions. As examples, we obtain temperature-strain phase diagrams of ferroelectric PbTiO 3 , strongly correlated VO 2 , and unconventional ferroelectric Hf 0.5 Zr 0.5 O 2 . We reveal the analogs of the Gibbs phase rules, multiple- and multi-critical points, common-tangent construction, and level rule in strain equilibria to those in the familiar chemical phase equilibria. Finally, our strain equilibria theory offers a powerful framework for predicting the thermodynamic stability of structural phases and domains in strained solids and for guiding the strain engineering of their functional properties.

36 MATERIALS SCIENCE↗

Origin of Phase Separation in Ni-Rich Layered Oxide Cathode Materials During Electrochemical Cycling

In intercalation materials, the kinetics and uniformity of mass transport across the nanocrystalline domains dictate the structural reversibility and transport capability at the macroscopic level. (De)intercalation-induced interlayer disintegrations exhibit anisotropic crystallite size change. Due to the anisotropic mass transport mechanism, separated phases are inherently crystallographically oriented. One such material is LiNi $1–x–y$ Mn $x$ Co $y$ O 2 , which plays a pivotal role in advanced Li-ion batteries but suffers from severe phase inhomogeneities under fast charge or electrochemical aging. Here, using operando synchrotron techniques, we probe the mechanistic origins of the compositional and orientational-dependent phase separations during the electrochemical cycling of LiNi 0.8 Mn 0.1 Co 0.1 O 2 by comprehensive analysis of both in-plane and out-of-plane reflections. In the H2/H3 phase regime, in-plane domain propagation occurs due to increased covalency despite the severe decay of interlayer crystallographic order, resulting in the change of crystalline domain shape from 3D spheres to two-dimensional nanosheets. The crystallographically selective XRD line splitting is linked to the geometry of the facets as mass transfers along the ab plane. In conclusion, this work provides mechanistic insights into crystallographic orientation-dependent phase inhomogeneity under fast charge and extended cycling.

36 MATERIALS SCIENCE↗

Structural and Optical Properties of High Entropy (La,Lu,Y,Gd,Ce)AlO 3 Perovskite Thin Films

Mixtures of Ce-doped rare-earth aluminum perovskites are drawing a significant amount of attention as potential scintillating devices. However, the synthesis of complex perovskite systems leads to many challenges. Designing the A-site cations with an equiatomic ratio allows for the stabilization of a single-crystal phase driven by an entropic regime. This work describes the synthesis of a highly epitaxial thin film of configurationally disordered rare-earth aluminum perovskite oxide (La 0.2 Lu 0.2 Y 0.2 Gd 0.2 Ce 0.2 )AlO 3 and characterizes the structural and optical properties. The thin films exhibit three equivalent epitaxial domains having an orthorhombic structure resulting from monoclinic distortion of the perovskite cubic cell. An excitation of 286.5 nm from Gd 3+ and energy transfer to Ce 3+ with 405 nm emission are observed, which represents the potential for high-energy conversion. These experimental results also offer the pathway to tunable optical properties of high-entropy rare-earth epitaxial perovskite films for a range of applications.

36 MATERIALS SCIENCE↗

Structural insights into photoactivation of plant Cryptochrome-2

Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal Structure and Characterization of Human Heavy-Chain Only Antibodies Reveals a Novel, Stable Dimeric Structure Similar to Monoclonal Antibodies

We report the novel crystal structure and characterization of symmetrical, homodimeric humanized heavy-chain-only antibodies or dimers (HC2s). HC2s were found to be significantly coexpressed and secreted along with mAbs from transient CHO HC/LC cotransfection, resulting in an unacceptable mAb developability attribute. Expression of full-length HC2s in the absence of LC followed by purification resulted in HC2s with high purity and thermal stability similar to conventional mAbs. The V H and C H 1 portion of the heavy chain (or Fd) was also efficiently expressed and yielded a stable, covalent, and reducible dimer (Fd2). Mutagenesis of all heavy chain cysteines involved in disulfide bond formation revealed that Fd2 intermolecular disulfide formation was similar to Fabs and elucidated requirements for Fd2 folding and expression. For one HC2, we solved the crystal structure of the Fd2 domain to 2.9 Å, revealing a highly symmetrical homodimer that is structurally similar to Fabs and is mediated by conserved (C H 1) and variable (V H ) contacts with all CDRs positioned outward for target binding. Interfacial dimer contacts revealed by the crystal structure were mutated for two HC2s and were found to dramatically affect HC2 formation while maintaining mAb bioactivity, offering a potential means to modulate novel HC2 formation through engineering. These findings indicate that human heavy-chain dimers can be secreted efficiently in the absence of light chains, may show good physicochemical properties and stability, are structurally similar to Fabs, offer insights into their mechanism of formation, and may be amenable as a novel therapeutic modality.

60 APPLIED LIFE SCIENCES↗

Structural Basis for the Catalytic Activity of Human SER/THR Protein Phosphatase-5

Serinekhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth. Here we report the 1.6 Angstrom resolution crystal structure of PP5 catalytic domain with metal and phosphate ions in the active site. The structure reveals a mechanism for PPS-mediated catalysis that requires the precise positioning of two metal ions within a conserved Asp(sup 271)-M(sub 1),-M(sub 2)-His(sup 427)-W(sup 2)-His(sup 304)-Asp(sup 274) catalytic motif, and provides a structural basis for the exceptional catalytic proficiency of protein phosphatases placing them among the most powerful catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of PP5 should aid development of specific inhibitors.

Swingle, M. R.↗

Modeling of Structural-Acoustic Interaction Using Coupled FE/BE Method and Control of Interior Acoustic Pressure Using Piezoelectric Actuators

A coupled finite element (FE) and boundary element (BE) approach is presented to model full coupled structural/acoustic/piezoelectric systems. The dual reciprocity boundary element method is used so that the natural frequencies and mode shapes of the coupled system can be obtained, and to extend this approach to time dependent problems. The boundary element method is applied to interior acoustic domains, and the results are very accurate when compared with limited exact solutions. Structural-acoustic problems are then analyzed with the coupled finite element/boundary element method, where the finite element method models the structural domain and the boundary element method models the acoustic domain. Results for a system consisting of an isotropic panel and a cubic cavity are in good agreement with exact solutions and experiment data. The response of a composite panel backed cavity is then obtained. The results show that the mass and stiffness of piezoelectric layers have to be considered. The coupled finite element and boundary element equations are transformed into modal coordinates, which is more convenient for transient excitation. Several transient problems are solved based on this formulation. Two control designs, a linear quadratic regulator (LQR) and a feedforward controller, are applied to reduce the acoustic pressure inside the cavity based on the equations in modal coordinates. The results indicate that both controllers can reduce the interior acoustic pressure and the plate deflection.

Mei, Chuh↗

Neural networks for structural design - An integrated system implementation

The development of powerful automated procedures to aid the creative designer is becoming increasingly critical for complex design tasks. In the work described here Artificial Neural Nets are applied to acquire structural analysis and optimization domain expertise. Based on initial instructions from the user an automated procedure generates random instances of structural analysis and/or optimization 'experiences' that cover a desired domain. It extracts training patterns from the created instances, constructs and trains an appropriate network architecture and checks the accuracy of net predictions. The final product is a trained neural net that can estimate analysis and/or optimization results instantaneously.

Berke, Laszlo↗

Driving magnetic domains at the nanoscale by interfacial strain-induced proximity

Here, we investigate the local nanoscale changes of the magnetic anisotropy of a Ni film subject to an inverse magnetostrictive effect by proximity to a V 2 O 3 layer. Using temperature-dependent photoemission electron microscopy (PEEM) combined with X-ray magnetic circular dichroism (XMCD), direct images of the Ni spin alignment across the first-order structural phase transition (SPT) of V 2 O 3 were obtained. We find an abrupt temperature-driven reorientation of the Ni magnetic domains across the SPT, which is associated with a large increase of the coercive field. Moreover, angular dependent ferromagnetic resonance (FMR) shows a remarkable change in the magnetic anisotropy of the Ni film across the SPT of V 2 O 3 . Micromagnetic simulations based on these results are in quantitative agreement with the PEEM data. Direct measurements of the lateral correlation length of the Ni domains from XMCD images show an increase of almost one order of magnitude at the SPT compared to room temperature, as well as a broad spatial distribution of the local transition temperatures, thus corroborating the phase coexistence of Ni anisotropies caused by the V 2 O 3 SPT. We show that the rearrangement of the Ni domains is due to strain induced by the oxide layers’ structural domains across the SPT. Our results illustrate the use of alternative hybrid systems to manipulate magnetic domains at the nanoscale, which allows for engineering of coercive fields for novel data storage architectures.

36 MATERIALS SCIENCE↗

Coupled Fluid-Structure Interaction Analysis of Solid Rocket Motor with Flexible Inhibitors

Flexible inhibitors are generally used in solid rocket motors (SRMs) as a means to control the burning of propellant. Vortices generated by the flow of propellant around the flexible inhibitors have been identified as a driving source of instabilities that can lead to thrust oscillations in launch vehicles. Potential coupling between the SRM thrust oscillations and structural vibration modes is an important risk factor in launch vehicle design. As a means to predict and better understand these phenomena, a multidisciplinary simulation capability that couples the NASA production CFD code, Loci/CHEM, with CFDRC's structural finite element code, CoBi, has been developed. This capability is crucial to the development of NASA's new space launch system (SLS). This paper summarizes the efforts in applying the coupled software to demonstrate and investigate fluid-structure interaction (FSI) phenomena between pressure waves and flexible inhibitors inside reusable solid rocket motors (RSRMs). The features of the fluid and structural solvers are described in detail, and the coupling methodology and interfacial continuity requirements are then presented in a general Eulerian-Lagrangian framework. The simulations presented herein utilize production level CFD with hybrid RANS/LES turbulence modeling and grid resolution in excess of 80 million cells. The fluid domain in the SRM is discretized using a general mixed polyhedral unstructured mesh, while full 3D shell elements are utilized in the structural domain for the flexible inhibitors. Verifications against analytical solutions for a structural model under a steady uniform pressure condition and under dynamic modal analysis show excellent agreement in terms of displacement distribution and eigenmode frequencies. The preliminary coupled results indicate that due to acoustic coupling, the dynamics of one of the more flexible inhibitors shift from its first modal frequency to the first acoustic frequency of the solid rocket motor. This insight could have profound implications for SRM and flexible inhibitor designs for current and future launch vehicles including SLS.

Yang, H. Q.↗