Thermo-optoplasmonic single-molecule sensing on optical microcavities

This is the final version. Available on open access from the American Chemical Society via the DOI in this recordWhispering-gallery-mode (WGM) resonators are powerful instruments for single-molecule sensing in biological and biochemical investigations. WGM sensors leveraged by plasmonic nanostructures, known as optoplasmonic sensors, provide sensitivity down to single atomic ions. In this article, we describe that the response of optoplasmonic sensors upon the attachment of single protein molecules strongly depends on the intensity of WGM. At low intensity, protein binding causes red shifts of WGM resonance wavelengths, known as the reactive sensing mechanism. By contrast, blue shifts are obtained at high intensities, which we explain as thermo-optoplasmonic (TOP) sensing, where molecules transform absorbed WGM radiation into heat. To support our conclusions, we experimentally investigated seven molecules and complexes; we observed blue shifts for dye molecules, amino acids, and anomalous absorption of enzymes in the near-infrared spectral region. As an example of an application, we propose a physical model of TOP sensing that can be used for the development of single-molecule absorption spectrometers.Engineering and Physical Sciences Research Council (EPSRC)Biotechnology and Biological Sciences Research Council (BBSRC

Single Molecule Thermodynamic Penalties Applied to Enzymes by Whispering Gallery Mode Biosensors

This is the final version. Available on open access from Wiley via the DOI in this recordData Availability Statement: The data that support the findings of this study are available in the supplementary material of this article.Optical microcavities, particularly whispering gallery mode (WGM) microcavities enhanced by plasmonic nanorods, are emerging as powerful platforms for single-molecule sensing. However, the impact of optical forces from the plasmonic near field on analyte molecules is inadequately understood. Using a standard optoplasmonic WGM single-molecule sensor to monitor two enzymes, both of which undergo an open-to-closed-to-open conformational transition, the work done on an enzyme by the WGM sensor as atoms of the enzyme move through the electric field gradient of the plasmonic hotspot during conformational change has been quantified. As the work done by the sensor on analyte enzymes can be modulated by varying WGM intensity, the WGM microcavity system can be used to apply free energy penalties to regulate enzyme activity at the single-molecule level. The findings advance the understanding of optical forces in WGM single-molecule sensing, potentially leading to the capability to precisely manipulate enzyme activity at the single-molecule level through tailored optical modulation.Biotechnology and Biological Sciences Research Council (BBSRC)Engineering and Physical Sciences Research Council (EPSRC

Multi-objective aerodynamic shape optimization of small livestock trailers

This paper presents a formal optimization study of the design of small livestock trailers, within which the majority of animals are transported to market in the United Kingdom. The benefits of employing a headboard fairing to reduce aerodynamic drag without compromising the ventilation of the animals’ micro-climate are investigated using a multi-stage process involving Computational Fluid Dynamics (CFD), Optimal Latin Hypercube (OLH), Design of Experiments (DoE) and Moving Least Squares (MLS) metamodels. Fairings are parameterised in terms of three design variables and CFD solutions are obtained at 50 permutations of design variables. Both global and local search methods are employed to locate the global minimum from metamodels of the objective functions and a Pareto front is generated. The importance of carefully selecting an objective function is demonstrated and optimal fairing designs, offering drag reductions in excess of 5% without compromising animal ventilation, are presented

The curse of numerical noise and implications for CFD-based design optimization

Numerical noise is an unavoidable by-product of Computational Fluid Dynamics (CFD) simulations which, in the context of design optimization, may lead to challenges in finding optimum designs. This article draws attention to this issue by illustrating the difficulties it can cause for road vehicle aerodynamics simulations. Firstly, a benchmark problem, flow past the Ahmed body, is used to highlight the effect of numerical noise on the calculation of aerodynamic drag. A series of simulations are conducted using three commonly employed Reynolds-Averaged Navier-Stokes (RANS) based turbulence models. Noise amplitudes of up to 22% are evident and the level of noise depends on the combination of turbulence model and grid used. Overall the Spalart Allmaras model is shown to be the least susceptible to noise levels for this particular application. Secondly, multi-objective aerodynamic shape optimization is applied to a low-drag aerodynamic fairing for a livestock trailer. The fairing is parameterised in terms of three design variables. Moving Least Squares (MLS) metamodels are constructed from 50 high-fidelity CFD solutions for two objective functions. Subsequent optimization is successful for the first objective, however numerical noise levels in excess of 7% are found to be problematic for the second one. A deliberate revision to the problem reduces the amount of noise present and leads to success with the construction of a small Pareto Front. Further analysis underlines the inherent capability of MLS metamodels in dealing with noisy CFD responses. Suggestions are also made to improve the chances of success for future investigations