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Annual Symposium

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10:00-10:40 Rakesh Arul – Bridging the visible and invisible worlds by looking through gold nanoparticles

Looking at the world with infrared (IR) light enables medical professionals to identify diseases, environmental scientists to monitor greenhouse gases, and the new James Webb Space Telescope to view the early universe. However, unlike visible light detection, IR detection is not widely applied due to existing technologies being inefficient, prohibitively expensive, and impractical. To circumvent this, we take advantage of the high efficiency of visible silicon detectors to help us detect IR. This can be accomplished using molecules that simultaneously absorb both visible and IR light and subsequently emit visible luminescence. While theoretically proposed in 1959 [1], realising this has proved challenging due to the fundamental mismatch between the wavelengths involved of visible (500 nm), IR light (10,000 nm) and molecular sizes (1 nm). To solve this problem, we use nanoparticle assemblies that can simultaneously squeeze visible and IR light down to the scale of a single molecule. Firstly, we use micron-sized spheres on a mirror to create nanocavities that trap IR light to the atomic limit and show conversion of IR light to visible light from a single molecule [2]. We termed this process mid-infrared vibrationally assisted luminescence [3]. Next, to expand to larger scale IR sensing, we use self-assembled Au nanoparticle multilayers which support collective plasmon-polariton resonances and show world record-breaking IR optical field enhancements [4].

References [1] Bloembergen, N. (1959). Solid state infrared quantum counters. Physical Review Letters, 2(3), 84. [2] Chikkaraddy, R., Arul, R., Jakob, L. A., & Baumberg, J. J. (2022). Single-molecule mid-IR detection through vibrationally assisted luminescence. arXiv preprint:2205.07792. [3] Arul, R., Baumberg, J.J., Chikkaraddy, R., & Xomalis, A. Mid-infrared detector (14 Mar 2022). UK Patent Application No. 2203507.5. [4] Arul, R., Benjamin-Grys, D., Chikkaraddy, R., Mueller, N. S., Xomalis, A., Miele, E., Euser, T.E. & Baumberg, J. J. (2022). Giant mid-IR resonant coupling to molecular vibrations in sub-nm gaps of plasmonic multilayer metafilms. Light: Science and Applications. 11, 281.

10:40-11:20 Dorothea Boeken – Understanding Alzheimer’s Disease, one molecule at a time

Alzheimer’s disease is currently one of the leading causes of death worldwide, yet the underlying mechanisms of the disease remain to be understood. One of the key signs of the disease is that a protein named tau starts to accumulate in neurons, leading to their death and irreversible neurodegeneration. We are trying to develop techniques that allow us to look at those tau deposits at the molecular level and characterise them one by one. By doing this, we can pinpoint the most harmful types of tau deposits and gain a better understanding of how the disease develops. Further, these tools are highly promising in diagnostics for the early detection of Alzheimer’s disease in blood samples.

11:20-12:00 Savvas Constantinou – Remote Sensing of Exoplanet Atmospheres with JWST Transmission Spectroscopy

The James Webb Space Telescope revolution has begun. Offering a generational improvement in sensitivity, wavelength coverage and resolution, JWST is set to revolutionise our understanding of exoplanet atmospheres. Taking full advantage of such high-quality observations, however, requires a significant advancement in the sophistication of atmospheric retrievals, the tools used to constrain atmospheric properties from observations. In this talk I will give an overview of the advances that exoplanet transmission spectroscopy and atmospheric retrievals have enabled over the last decade. I will then present my own work, seeking to understand what atmospheric constraints JWST enables and what features a next-generation atmospheric retrieval framework should have. To do this, I carried out the first detailed retrieval study on the JWST transmission spectrum of the hot Saturn WASP -39b obtained through the Early Release Science programme. This results in detections and abundance constraints for CO2 , SO2, H2O and CO, as well as tentative indications of H2S . Their concentrations indicate elemental abundances consistent with Saturn’s metallicity. I will also present how such high quality data enable constraints on the properties of Mie scattering aerosols, including their composition and modal size, motivating their consideration in next-generation retrieval frameworks. Lastly, I will discuss key lessons learnt from these first retrievals on JWST spectra of exoplanets.

Lunch Break

13:30-13:50 Ruslan Kotlyarov – Found In Translation: Using Language Models To Predict C–H Borylation Regioselectivity

By treating chemical reactions as a machine translation task, it is possible to successfully predict a wide range of chemical reaction outcomes using text-based representation as only input (Schwaller 2019). We investigated how encoder-decoder transformer models can be fine-tuned to predict regioselectivity for the pharmaceutically relevant C–H borylation. We found our model performance is comparable to state of the art deep learning models trained on the same amount of data but further investigation is needed on how well it generalises to new substrates.

13:50-14:30 Kyle Frohna – A Glorious Mess: Understanding Nanoscale Disorder in Next-Generation Solar Cells

In the pursuit of cheaper, flexible and higher efficiency solar panels, scientists around the world have been developing new materials to challenge and potentially overthrow the incumbent silicon panels. These next generation solar cells are thin films (normally ~500 times thinner than Silicon cells), are often deposited with low cost techniques and consist of materials such as organics, copper indium gallium selenide or the focus of this talk, metal-halide perovskites. Perovskites in particular have shown the fastest increase in solar cell performance in history. While these materials all share promise for photovoltaics, they also have in common massive disorder on multiple length scales ranging from macroscopic down to the atomic. This disorder has large implications for their operational stability and their optical/electronic behaviour. In this talk, I will present some of our work on metal halide perovskite solar cells to uncover the origins of this messiness at the smallest length scales and how it affects the behaviour of the solar cells and their stability.

14:30-15:15 Prof. David Baulcombe – Food security: the pros and cons of GM and gene editing as solutions to disease in crops

15:15-15:55 Abhishek Upadhyay – Biological clocks and timers – from fungi, plants to animals – a signature of life

Chronobiology is the study of periodically occurring physiological, metabolic, and behavioral processes in living organisms. Moreover, Biological clocks and timers are part and parcel of design principle of life on Earth.

Notably, Circadian rhythms (24 hr oscillations) have evolved across cyanobacteria, algae, fungi, insects, plants and mammals based on daily interactions between internal timing and environmental cues. Molecular circadian oscillators consist of a transcription-translation feedback loop (TTFL) allowing self-sustained rhythms. How these rhythms are generated and how they are entrained (“synchronized”“) by external zeitgebers i.e., light, temperature, nutrients, is poorly understood.

Furthermore, many developmental processes repeat rhythmically. For example, rhythmicity in somite formation is ensured through a ‘clock’ mechanism where a Hes transcription factor inhibits its own transcription, yielding oscillatory activity. To what degree such genetically-encoded oscillators originate and function in other developmental rhythms contexts, for example C. elegans oscillator (8 hr periodicity), is unknown.

I took up multiple theoretical and experimental approaches and utilised multiple model organisms across the kingdoms of life: filamentous fungi (Neurospora crassa), terrestrial plant (Arabidopsis thaliana) and nematode animal (Caenorhabditis elegans) to study above mentioned questions. My conceptual, semi-quantitative, and data-driven quantitative mathematical modelling, and time course omics experiments combined with computational data analysis revealed answers to those questions.

I will present my published and unpublished results to discuss how multiple protein phosphorylations provide long delay and act as molecular switches required for the origin of circadian rhythms. Moreover, I will discuss how temperature cycles put the molecular circadian clockwork in phase with external signal. Furthermore, I will share my discovery of oscillations at proteome and phosphoproteome levels in a developmental clock

Tea Break

16:10-16:30 Alberto Echevarría-Poza – MRI of injured plant cell walls?

Have you ever wondered why apples are crunchy? Or why wood is so hard? The answer is… the plant cell wall! You probably have heard of cellulose before, but, that’s just one out of the many, many different, essential polymers making up the plant cell wall. I used MRI , oops, I mean, NMR to investigate the interaction between those components at a molecular level, and, particularly how the conformations of cellulose and xylan (the second most abundant polysaccharide in the cell wall and… on earth!) seem to change upon mutations that result in shorter and scarcer xylan.

16:30-17:15 Prof. Grae Worster – Aerogels

17:15-17:55 Prof. Judith Driscoll – Memory materials

[Some abstracts are TBD ]

This talk is part of the Trinity College Science Society 2022-23 series.

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