Controlling trapping potentials and stray electric fields in a microfabricated ion trap through design and compensation

Recent advances in quantum information processing with trapped ions have demonstrated the need for new ion trap architectures capable of holding and manipulating chains of many (>10) ions. Here we present the design and detailed characterization of a new linear trap, microfabricated with scalable complementary metal-oxide-semiconductor (CMOS) techniques, that is well-suited to this challenge. Forty-four individually controlled DC electrodes provide the many degrees of freedom required to construct anharmonic potential wells, shuttle ions, merge and split ion chains, precisely tune secular mode frequencies, and adjust the orientation of trap axes. Microfabricated capacitors on DC electrodes suppress radio-frequency pickup and excess micromotion, while a top-level ground layer simplifies modeling of electric fields and protects trap structures underneath. A localized aperture in the substrate provides access to the trapping region from an oven below, permitting deterministic loading of particular isotopic/elemental sequences via species-selective photoionization. The shapes of the aperture and radio-frequency electrodes are optimized to minimize perturbation of the trapping pseudopotential. Laboratory experiments verify simulated potentials and characterize trapping lifetimes, stray electric fields, and ion heating rates, while measurement and cancellation of spatially-varying stray electric fields permits the formation of nearly-equally spaced ion chains.Comment: 17 pages (including references), 7 figure

Demonstration of integrated microscale optics in surface-electrode ion traps

In ion trap quantum information processing, efficient fluorescence collection is critical for fast, high-fidelity qubit detection and ion-photon entanglement. The expected size of future many-ion processors require scalable light collection systems. We report on the development and testing of a microfabricated surface-electrode ion trap with an integrated high numerical aperture (NA) micromirror for fluorescence collection. When coupled to a low NA lens, the optical system is inherently scalable to large arrays of mirrors in a single device. We demonstrate stable trapping and transport of 40Ca+ ions over a 0.63 NA micromirror and observe a factor of 1.9 enhancement in photon collection compared to the planar region of the trap.Comment: 15 pages, 8 figure

Precision Needle-Punch Tumor Enrichment From Paraffin Blocks Improves the Detection of Clinically Actionable Genomic Alterations and Biomarkers

BACKGROUND: While many molecular assays can detect mutations at low tumor purity and variant allele frequencies, complex biomarkers such as tumor mutational burden (TMB), microsatellite instability (MSI), and genomic loss of heterozygosity (gLOH) require higher tumor purity for accurate measurement. Scalable, quality-controlled, tissue-conserving methods to increase tumor nuclei percentage (TN%) from tumor specimens are needed for complex biomarkers and hence necessary to maximize patient matching to approved therapies or clinical trial enrollment. We evaluated the clinical utility and performance of precision needle-punch enrichment (NPE) compared with traditional razor blade macroenrichment of tumor specimens on molecular testing success. METHODS: Pathologist-directed NPE was performed manually on formalin-fixed, paraffin embedded (FFPE) blocks. Quality control of target capture region and quantity of residual tumor in each tissue block was determined via a post-enrichment histologic slide recut. Resultant tumor purity and biomarker status were determined by the computational analysis pipeline component of the FDA-approved next-generation sequencing (NGS) assay, FoundationOne RESULTS: In real-world clinical samples, enrichment rate via NPE was increased to ~50% over a 2.5-year period, exceeding the prior use of razor blade macro-enrichment ( CONCLUSIONS: Pathologist-directed precision enrichment from tissue blocks (aka NPE) increases tumor purity, and consequently, yields a greater number of successful tests and complex biomarker determinations. Moreover, this process is rapid, safe, inexpensive, scalable, and conserves patient surgical pathology material. NPE may constitute best practice with respect to enriching tumor cells from low-purity specimens for biomarker detection in molecular laboratories

Molecular and cellular mechanisms underlying the evolution of form and function in the amniote jaw.

The amniote jaw complex is a remarkable amalgamation of derivatives from distinct embryonic cell lineages. During development, the cells in these lineages experience concerted movements, migrations, and signaling interactions that take them from their initial origins to their final destinations and imbue their derivatives with aspects of form including their axial orientation, anatomical identity, size, and shape. Perturbations along the way can produce defects and disease, but also generate the variation necessary for jaw evolution and adaptation. We focus on molecular and cellular mechanisms that regulate form in the amniote jaw complex, and that enable structural and functional integration. Special emphasis is placed on the role of cranial neural crest mesenchyme (NCM) during the species-specific patterning of bone, cartilage, tendon, muscle, and other jaw tissues. We also address the effects of biomechanical forces during jaw development and discuss ways in which certain molecular and cellular responses add adaptive and evolutionary plasticity to jaw morphology. Overall, we highlight how variation in molecular and cellular programs can promote the phenomenal diversity and functional morphology achieved during amniote jaw evolution or lead to the range of jaw defects and disease that affect the human condition