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At least 1,567 records · Page 87

Quantifying data retention of perpendicular spin-transfer-torque magnetic random access memory chips using an effective thermal stability factor method

The thermal stability of perpendicular Spin-Transfer-Torque Magnetic Random Access Memory (STT-MRAM) devices is investigated at chip level. Experimental data are analyzed in the framework of the Néel-Brown model including distributions of the thermal stability factor Δ. We show that in the low error rate regime important for applications, the effect of distributions of Δ can be described by a single quantity, the effective thermal stability factor Δ{sub eff}, which encompasses both the median and the standard deviation of the distributions. Data retention of memory chips can be assessed accurately by measuring Δ{sub eff} as a function of device diameter and temperature. We apply this method to show that 54 nm devices based on our perpendicular STT-MRAM design meet our 10 year data retention target up to 120 °C.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Lorentz factor determination for local electric fields in semiconductor devices utilizing hyper-thin dielectrics

The local electric field (the field that distorts, polarizes, and weakens polar molecular bonds in dielectrics) has been investigated for hyper-thin dielectrics. Hyper-thin dielectrics are currently required for advanced semiconductor devices. In the work presented, it is shown that the common practice of using a Lorentz factor of L = 1/3, to describe the local electric field in a dielectric layer, remains valid for hyper-thin dielectrics. However, at the very edge of device structures, a rise in the macroscopic/Maxwell electric field E{sub diel} occurs and this causes a sharp rise in the effective Lorentz factor L{sub eff}. At capacitor and transistor edges, L{sub eff} is found to increase to a value 2/3 < L{sub eff} < 1. The increase in L{sub eff} results in a local electric field, at device edge, that is 50%–100% greater than in the bulk of the dielectric. This increase in local electric field serves to weaken polar bonds thus making them more susceptible to breakage by standard Boltzmann and/or current-driven processes. This has important time-dependent dielectric breakdown (TDDB) implications for all electronic devices utilizing polar materials, including GaN devices that suffer from device-edge TDDB.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Effective bichromatic potential for ultra-high Q-factor photonic crystal slab cavities

We introduce a confinement mechanism in photonic crystal slab cavities, which relies on the superposition of two incommensurate one-dimensional lattices in a line-defect waveguide. It is shown that the resulting photonic profile realizes an effective quasi-periodic bichromatic potential for the electromagnetic field confinement yielding extremely high quality (Q) factor nanocavities, while simultaneously keeping the mode volume close to the diffraction limit. We apply these concepts to pillar- and hole-based photonic crystal slab cavities, respectively, and a Q-factor improvement by over an order of magnitude is shown over existing designs, especially in pillar-based structures. Thanks to the generality and easy adaptation of such confinement mechanism to a broad class of cavity designs and photonic lattices, this work opens interesting routes for applications where enhanced light–matter interaction in photonic crystal structures is required.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Calculation of self–shielding factor for neutron activation experiments using GEANT4 and MCNP

The neutron self–shielding factor G as a function of the neutron energy was obtained for 14 pure metallic samples in 1000 isolethargic energy bins from 1·10{sup −5}eV to 2·10{sup 7}eV using Monte Carlo simulations in GEANT4 and MCNP6. The comparison of these two Monte Carlo codes shows small differences in the final self–shielding factor mostly due to the different cross section databases that each program uses.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

On the ideality factor of the radiative recombination current in semiconductor light-emitting diodes

While there have been many discussions on the standard Si pn-diodes, little attention has been paid and confusion still arises on the ideality factor of the radiative recombination current in semiconductor light-emitting diodes (LEDs). In this letter, we theoretically demonstrate and experimentally confirm by using blue and infrared semiconductor LEDs that the ideality factor of the radiative recombination current is unity especially for low-current-density ranges. We utilize the data of internal quantum efficiency measured by the temperature-dependent electroluminescence to separate the radiative current component from the total current.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Influence of the polarization anisotropy on the linewidth enhancement factor and reflection sensitivity of 1.55- μ m InP-based InAs quantum dash lasers

This work investigates the effect of the polarization anisotropy on the linewidth enhancement factor and the reflection sensitivity of InAs/InP quantum dash semiconductor lasers. The results show that the small linewidth enhancement factor and high stability against external optical feedback are obtained for nanostructures oriented perpendicular to the cavity axis as opposed to those oriented parallel to the cavity axis. Effective simulations on the critical feedback level of these two lasers are also in agreement with experimental results. Such anisotropy is attributed to the polarization dependence of the transition matrix element in these quantum nanostructures.

Dong, B. (ORCID:0000000158266723)↗

Heterostructure design to achieve high quality, high density GaAs 2D electron system with g -factor tending to zero

Hydrostatic pressure is a useful tool that can tune several key parameters in solid state materials. For example, the Landé g-factor in GaAs two-dimensional electron systems (2DESs) is expected to change from its bulk value g ≃ -0.44 to zero and even to positive values under sufficiently large hydrostatic pressure. Although this presents an intriguing platform to investigate electron-electron interaction in a system with g = 0, studies are quite limited because the GaAs 2DES density decreases significantly with increasing hydrostatic pressure. Here, we show that a simple model, based on pressure-dependent changes in the conduction band alignment, quantitatively explains this commonly observed trend. Furthermore, we demonstrate that the decrease in the 2DES density can be suppressed by more than a factor of 3 through an innovative heterostructure design.

Physics↗

Intrinsic quality factor extraction of multi-port cavity with arbitrary coupling

In this work, we derived S-parameter based expressions for the intrinsic quality factor of an arbitrary coupled multiport microwave cavity and a non-ideal test fixture. Practical accuracy limitations of the obtained expressions specifically for superconducting accelerator cavities were evaluated both analytically and with the simulation software. The resulting formulas can be used to extract the intrinsic quality factor of normal-conducting and superconducting cavities directly from the calibrated S-parameter measurements.

43 PARTICLE ACCELERATORS↗

Increased thermal conductivity and decreased electron–phonon coupling factor of the aluminum scandium intermetallic phase (Al 3 Sc) compared to solid solutions

Aluminum scandium alloys and their intermetallic phases have arisen as potential candidates for the next generation of electrical interconnects. Here, in this work, we measure the in-plane thermal conductivity and electron–phonon coupling factor of aluminum scandium alloy thin films deposited at different temperatures, where the temperature is used to control the grain size and volume fraction of the Al 3 Sc intermetallic phase. As the Al 3 Sc intermetallic formation increases with higher deposition temperature, we measure increasing in-plane thermal conductivity and a decrease in the electron–phonon coupling factor, which corresponds to an increase in grain size. Our findings demonstrate the role that chemical ordering from the formation of the intermetallic phase has on thermal transport.

Chemical elements↗

Factor of spontaneous emission into the optical dielectric waveguide mode

Within the framework of a complete vector analysis, an expression for the factor of spontaneous emission into the transverse mode of a dielectric waveguide is found. The results are compared with those previously obtained in the framework of the scalar approximation. It is shown that their most significant quantitative difference is possible for waveguides used in diode lasers and amplifiers in which the transverse beam size is commensurable with the wavelength. The conditions for the applicability of the scalar approximation for calculating the spontaneous emission factor are obtained. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space

Many genomes contain families of paralogs—proteins with divergent function that evolved from a common ancestral gene after a duplication event. To understand how paralogous transcription factors evolve divergent DNA specificities, we examined how the glucocorticoid receptor and its paralogs evolved to bind activating response elements [(+)GREs] and negative glucocorticoid response elements (nGREs). We show that binding to nGREs is a property of the glucocorticoid receptor (GR) DNA-binding domain (DBD) not shared by other members of the steroid receptor family. Using phylogenetic, structural, biochemical, and molecular dynamics techniques, we show that the ancestral DBD from which GR and its paralogs evolved was capable of binding both nGRE and (+)GRE sequences because of the ancestral DBD’s ability to assume multiple DNA-bound conformations. Subsequent amino acid substitutions in duplicated daughter genes selectively restricted protein conformational space, causing this dual DNA-binding specificity to be selectively enhanced in the GR lineage and lost in all others. Key substitutions that determined the receptors’ response element-binding specificity were far from the proteins’ DNA-binding interface and interacted epistatically to change the DBD’s function through DNA-induced allosteric mechanisms. These amino acid substitutions subdivided both the conformational and functional space of the ancestral DBD among the present-day receptors, allowing a paralogous family of transcription factors to control disparate transcriptional programs despite high sequence identity.

59 BASIC BIOLOGICAL SCIENCES↗

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set of Drosophila early embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation of Drosophila expression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. In conclusion, the performance of PP with the Drosophila data suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗

Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity

Significance Plants both control and are controlled by the global climate. Grasses in natural and agricultural systems participate in the exchange of atmospheric CO 2 for biosphere-derived oxygen and water vapor via microscopic epidermal valves (stomata), but how these stomata are made in grasses is unknown. Using genetic screens and targeted genome editing, we identify and characterize master transcriptional regulators of stomatal initiation in the wheat relative Brachypodium . Surprisingly, the unique stomatal form and pattern of grasses is regulated by orthologs of Arabidopsis stomatal basic helix–loop–helix (bHLH) transcription factors, although the function of individual genes and regulation of their protein products have diverged. This finding suggests that the stomatal core bHLH transcription factors are excellent breeding targets to enhance performance in grasses.

Raissig, Michael T.↗

Photoprotection during iron deficiency is mediated by the bHLH transcription factors PYE and ILR3

Iron deficiency has many adverse effects on photosynthesis, which is not surprising given that 90% of foliar iron is found in the chloroplast. Although many iron-sparing mechanisms have been documented, a mechanistic understanding of how chloroplasts adapt to iron deficiency was lacking. Here, we show that the bHLH transcription factors ILR3 and PYE are required for photoprotection during iron deficiency. Changes in chloroplast morphology under the control of these transcription factors prevents the production of harmful reactive oxygen species and allows for repair of photosystem II. Understanding how plants adapt the photosynthetic machinery during iron deficiency may allow us to optimize plant growth in soils where iron is not bioavailable.

59 BASIC BIOLOGICAL SCIENCES↗

SHP2 genetic variants in NSML-associated RASopathies disrupt the PZR–IRX transcription factor signaling axis

Noonan syndrome with multiple lentigines (NSML) is a rare autosomal dominant disorder caused by mutations inPTPN11(protein tyrosine phosphatase nonreceptor type 11) which encodes for the protein tyrosine phosphatase, SHP2. Approximately 85% of NSML patients develop hypertrophic cardiomyopathy (HCM). Here, we show that SHP2 is recruited to tyrosyl phosphorylated protein-zero related (PZR) in NSML mice. This recruitment is required for the Iroquois homeobox (IRX) transcription factors 3 and 5 to suppress BMP10 which negatively regulates postnatal cardiac growth. The protein expression of IRX3 and IRX5 was elevated in hypertrophied NSML hearts. IRX3 and IRX5 upregulation was rescued in NSML mice harboring a knock-in mutation of PZR that fails to become tyrosyl phosphorylated and recruit SHP2. NSML mice treated with low-dose dasatinib also exhibited normalized IRX3 and IRX5 expression levels. Consistent with this, BMP10 expression levels were reduced in NSML mice and rescued in PZR tyrosyl phosphorylation-deficient and low-dose dasatinib-treated NSML mice. A crystal structure of the tandem SH2 domains of SHP2 bound to tyrosyl phosphorylated PZR reveals that recruitment constrains the open SHP2 conformation to facilitate cellular-Src (c-Src) binding. Disruption of c-Src binding to SHP2 abolished IRX activation and failure to suppress BMP10. Hence, NSML-associated SHP2 genetic variants disrupt IRX transcription factor signaling to BMP10, implicating this axis as a target for RASopathy-associated HCM.

Science & Technology - Other Topics↗

Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy

Rational design–guided improvement of protein thermostability typically requires identification of residues or regions contributing to instability and introduction of mutations into these residues or regions. One popular method, B-FIT, utilizes B-factors to identify unstable residues or regions and combines them with other strategies, such as directed evolution. Here, we performed structure-based engineering to improve the thermostability of the subtilisin E-S7 (SES7) peptidase. The B-value of each residue was redefined in a normalized B-factor calculation, which was implemented with a refined bioinformatics analysis strategy to identify the critical area (loop 158–162) related to flexibility and to screen for suitable thermostable motif sequences in the Protein Data Bank that can act as transplant loops. In total, we analyzed 445 structures and identified 29 thermostable motifs as candidates. Using these motifs as a starting point, we performed iterative homologous modeling to obtain a desirable chimera loop and introduced five different mutations into this loop to construct thermostable SES7 proteins. Differential scanning fluorimetry revealed increases of 7.3 °C in the melting temperature of an SES7 variant designated M5 compared with the WT. The X-ray crystallographic structure of this variant was resolved at 1.96 Å resolution. The crystal structure disclosed that M5 forms more hydrogen bonds than the WT protein, consistent with design and molecular dynamics simulation results. In summary, the modified B-FIT strategy reported here has yielded a subtilisin variant with improved thermostability and promising industrial applications, supporting the notion that this modified method is a powerful tool for protein engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences

Abstract The binding sites of transcription factors (TFs) in upstream DNA regions are called transcription factor binding sites (TFBSs). TFBSs are important elements for regulating gene expression. To date, there have been few studies on the profiles of TFBSs in plants. In total, 4,873 sequences with 5ʹ upstream regions from 8530 wheat fl-cDNA sequences were used to predict TFBSs. We found 4572 TFBSs for the MADS TF family, which was twice as many as for bHLH (1951), B3 (1951), HB superfamily (1914), ERF (1820), and AP2/ERF (1725) TFs, and was approximately four times higher than the remaining TFBS types. The percentage of TFBSs and TF members showed a distinct distribution in different tissues. Overall, the distribution of TFBSs in the upstream regions of wheat fl-cDNA sequences had significant difference. Meanwhile, high frequencies of some types of TFBSs were found in specific regions in the upstream sequences. Both TFs and fl-cDNA with TFBSs predicted in the same tissues exhibited specific distribution preferences for regulating gene expression. The tissue-specific analysis of TFs and fl-cDNA with TFBSs provides useful information for functional research, and can be used to identify relationships between tissue-specific TFs and fl-cDNA with TFBSs. Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes.

Chen, Zhen-Yong↗

High-throughput small-angle X-ray scattering reveals effective structure factor transitions linked to high-concentration antibody viscosity

High-concentration monoclonal antibody (mAb) formulations are often constrained by elevated viscosity, largely driven by protein–protein interactions, which complicates manufacturing and limits subcutaneous delivery. Early viscosity risk assessment is essential during discovery, yet traditional measurements require large sample volumes, and lack high-throughput capability. Here, we develop a high-throughput small-angle X-ray scattering (SAXS) protocol to detect mAb self-association at dilute concentrations, enabling early predictive insights into high-concentration viscosity. Synchrotron SAXS measurements were conducted for 21 mAbs formulated in a histidine buffer at pH 6.0. An initial subset of 10 mAbs analyzed across 1–150 mg/mL revealed that effective structure factor transitions in the low-q region, indicative of interparticle interactions, consistently emerged below 25 mg/mL. Subsequently, 11 additional mAbs were analyzed at 1–25 mg/mL using automated liquid handling and flow cells to enable high-throughput screening. High-viscosity mAbs exhibited detectable low-q upturns at concentrations ≤10 mg/mL, whereas low-viscosity mAbs showed downturns. A classification criterion based on effective structure factor transitions accurately classified all high- and low-viscosity mAbs at 150 mg/mL, offering a scalable, sample-efficient alternative to conventional methods. These results extend recent findings on the concentration-dependent sensitivity of SAXS to short-range attractions, demonstrating that they can emerge at lower concentrations than previously reported. This study presents the most comprehensive and diverse SAXS dataset for mAbs reported to date within a single formulation, providing a valuable resource for developing and validating coarse-grained models that can more accurately capture intermolecular interactions governing high-concentration solution behavior, thereby enabling rational antibody engineering and improved developability.

36 MATERIALS SCIENCE↗