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Rational Design of Nanoplasmonic Array Geometries for Biosensing

Background: Molecular diagnostics provide early and accurate diagnosis, which is essential for the prevention and treatment of infectious as well as chronic diseases. These tests are designed to detect disease-specific bioanalytes such as nucleic acid (DNA or RNA) or protein (antigens, antibodies) biomarkers. In the context of infectious disease diagnosis, nucleic acid-based detection methods are known to provide more specific and sensitive results. Here, the presence of a unique sequence belonging to the pathogenic genomic material is targeted to identify species, organism, genera and/or antimicrobial resistant gene markers. The majority of the common nucleic acid based diagnostic techniques require amplification (polymerase chain reaction, isothermal amplification etc.) of the pathogenic genetic material prior to detection impacting diagnostic speed, complexity, and cost thereby limiting ease of use. Thus, the development of simplified nucleic acid-based diagnostics that can be even used in resource-poor settings may hugely benefit patients across the globe. Nanopath is a molecular diagnostics company utilizing a solid-state nanosensor to enable sequence-specific detection of target nucleic acids without the need of amplification. These nanostructures enable ultra-sensitive biomarker detection using geometric, feature-dependent properties highly dependent on the local dielectric environment, allowing them to be sensitive to low concentration binding events. This paper describes an application of this approach to provide highly relevant clinical information within a single doctor’s office visit. Intro: The Nanopath team is in collaboration with NASA (National Aeronautics and Space Administration) and NIST (National Institute of Standards and Technology) to push the bounds of the fundamental physics associated with their biosensing platform. The ability of metals to support electromagnetic surface waves gives rise to surface plasmons when optically illuminated. This property, and its strong sensitivity to changes in the local refractive index, allows for the use of metal nanoparticles as ultra-sensitive transducers. In prior work by members of this team, ensembles of randomly oriented nanoparticles (i.e., colloidal nanorods dispersed on chip) were employed for sequence-specific nucleic acid sensing (1-3). While these particle sensors have the advantage of rapid fabrication, they suffer from low sensitivity and quality factor due to the random particle dispersity. In contrast, in this study we employ ordered array nanoparticle ensembles which can be used to improve sensor sensitivity and figure-of-merit. Study Methods Overview: In this talk, we detail the results of sensing experiments and computational simulations to outline a rational design of the structure of these plasmonic nanoparticle arrays for biomolecular sensing. Through simulation and experiment, we iteratively tailor nanostructure dimension to provide high quality signal and large resonance shifts upon modeled nucleic acid binding. In particular, full-wave electromagnetic simulations were conducted using Lumerical photonic simulation software in which periodic boundary conditions were applied in the x- and y- dimensions for each of the nanoplasmonic sensor geometries. To simulate the resonance response to changes in the bulk solution in contact with the sensor surface, the refractive index of the surrounding media was changed appropriately. Nucleic acid hybridization events were modeled using either using spherical structures approximating the relevant radius of genomic material as estimated by polymer models, or as conformal layers with the known refractive indices for nucleic acids. On the basis of initial simulations, nanosensors were fabricated using traditional electron-beam lithography protocols at NIST. To evaluate consensus between simulations and experiments, bulk sensing experiments were carried out in which the resonance peaks were obtained by submerging the sensors in refractive index standards. Key nanosensor characteristics including resonance peak locations, resonance peak shifts as a function of refractive index, and figure of merit (FOM) of extinction curves were examined between the experimental and simulation results prior to proceeding with simulations on additional geometries and more complex solution conditions, and further device fabrication. This iterative process is repeated toward a rational design of nanoplasmonic array geometries for biosensing optimizing response for targeted disease detection. In summary, this study puts forth a methodology for rational design and characterization of regularly spaced nanoparticle arrays for optics-based biosensing. The results of this study will allow for more informed design of nanostructure geometries towards sequence-specific nucleic acid detection. These improved designs have the potential to improve clinical sensitivity and limit-of-detection across disease indication.

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NASA NTRS2024

Testing of Advanced Capabilities to Enable In-time Safety Management and Assurance for Future Flight Operations

In order to refine an initial Concept of Operations, explore Concepts of Use, and expose/validate requirements for future In-Time Aviation Safety Management Systems (IASMS), testing architectures were created, along with a set of capabilities and underlying information exchange protocols. These systems were conceived and developed based on hazards associated with two envisioned urban area flight domains: (1) highly autonomous small uncrewed aerial systems (sUAS) operating at low altitudes, and (2) highly autonomous air taxis. The initial scope of this development is described in [1]; this report provides an update, focusing on the subsequent developments and test activities. As stated in [1], it is important to note that there are many capabilities already in use by the industry (or soon to be in use) that will play critical roles in future IASMS designs. Those reported here were developed to address a gap in the current state-of-the-art regarding specific hazards/risks, and/or to allow for investigation of the interplay between and across hazard types — particularly regarding how overall safety risk can be reduced or managed effectively. Results of testing and development activities are organized by the operational phase wherein a particular capability would be employed (i.e., preflight, in-flight, and post-flight/off-line). Pre-flight: A set of capabilities were developed to help mitigate safety risk prior to flight (e.g., during flight and mission planning). Results of testing summarize (1) validation activities to raise the Technology Readiness Level (TRL) and (2) evaluation activities where the capabilities were applied to flight/mission planning procedures and used by operators/pilots. For the latter, flight plans were automatically assessed, and operators/pilots were notified of hazardous flight segments so as to enable adjustment of the flight plan and re-evaluation, and/or to better inform go/no-go decisions. Capabilities addressed hazards associated with power consumption, third-party risk, wind, navigation system performance, radiofrequency interference, and proximity to geo-spatial threats (e.g., buildings, trees, and no-fly zones). In-flight: Flight experiments tested capabilities that detect and respond to hazards encountered during flight. In the first series, safety hazards were monitored and assessed onboard, and system-generated mitigation maneuvers were recorded (but not acted upon by the vehicle). In the second series, mitigation maneuver commands directed the aircraft in response to safety hazards (i.e., auto-mitigation). The sUAS used for testing is described in full, as is the test architecture, which included commercial avionics, research avionics, and onboard software designed to detect, assess, and respond to hazards. The onboard system was designed as a run-time assurance framework, consistent with [2] and supportive of both supervisory and automated modes. The primary functions included: real-time risk assessment (RTRA), auto-pilot monitoring, constraint monitoring, and contingency select/triggering. RTRA performs integrated risk assessment considering data from several hazard-related monitors (e.g., battery, motors, navigation, communications, population density, and loss-of-control). Post-flight/off-line: Data monitored and recorded during flights can enable IASMS capabilities that execute after flights have completed (or “off-line”). These include: (1) the ability to identify anomalies and trends that may only be observable when comparing data spanning a number of similar flights; (2) the ability to update and validate pre-flight and in-flight capabilities and any underlying models to improve their performance; (3) the ability to report anomalies/off-nominals that may indicate design changes or maintenance actions are needed; and (4) the ability for humans involved in operations to report safety-relevant observations to help in understanding the flight data and/or the operational context of a flight. Progress on three such capabilities is summarized; the first investigates anomaly detection given a limited set of flight logs and applies an approach previously used for space operations. The second explores what could be identified using a larger set of flight logs, including from web-based forums where flight logs are posted by sUAS autopilot users. The third creates a new means of collecting information on UAS incidents and accidents via the Aviation Safety Reporting System (ASRS).

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