Past research proposals test

Lead Supervisor: Claudia Bonfio, Department of Biochemistry
Co-supervisor: Katherine Stott, Department of Biochemistry

Brief summary
This project aims at assembling primitive cells capable of division in the absence of modern biochemical machinery. Our lab has so far focused on the ability of primitive lipids to organise in different lipid domains. We now aim to employ primitive coacervates to modulate the surface area-to-volume of primitive liposomes, ultimately leading to division. This project will provide:
i) an understanding on the molecular features that govern interactions between membrane-less and membrane-bound compartments,
ii) a library of coacervates able to affect the surface area-to-volume of liposomes
iii) optimised protocols for the spectroscopic characterisation and imaging of primitive cell models.

Importance of the area of research concerned
Throughout evolution, modern cells have developed sophisticated machinery to precisely divide their membrane-bound compartments and regulate them. Yet, the minimal set of cellular components available for primitive cells to drive their division is still unknown. This lack of understanding calls for fundamental studies seeking strategies for primitive cell division.

This project aims to address this knowledge gap by exploring the cooperative interactions between primitive compartments (i.e., membrane-bound and membrane-less compartments), and their impact on enzyme-free cellular division.

Our research will serve as a biochemical platform for probing the origin of cellular replication, and the principles leading to the emergence of living cells. Moreover, not only will this project explore the synergy between protocell models so far only considered antithetically. It will also offer a more complete picture of the transition from prebiotic chemistry to early life.

What will the student do?
The student will be able to develop biophysics and supramolecular chemistry skills, which can be applied to membrane-bound and membrane-less model compartments (i.e., liposomes and biomolecular condensates). Specifically, the student will investigate the compatibility of complex coacervates, made of short oligonucleotides and positively-charged peptides, and lipid membranes, composed of primitive lipids (e.g., medium-chain fatty acids, phosphatidic acids and more complex phospholipids). The student will design and develop real-time spectroscopy- and imaging-based protocols to study the  interactions between different primitive cell models. The project offers interactions with other groups across multiple departments, including Prof. Lorenzo Di Michele, Dr. Phil Holliger and Prof. Rosana Collepardo-Guevara.

References
Hargreaves W., Mulvihill S. and Deamer D. - Synthesis of phospholipids and membranes in prebiotic conditions. Nature 266, 78-80 (1977). https://doi.org/10.1038/266078a0
Bonfio C., Russell D.A., Green N.J., Mariani A. and Sutherland J.D. - Activation chemistry drives the emergence of functionalised protocells. Chem Sci. 11, 1068810697 (2020). https://doi.org/10.1039/D0SC04506C
Lloyd C.T., Iwig D.F., Wang B. et al. - Discovery, structure and mechanism of a tetraether lipid synthase. Nature 609, 197–203 (2022). https://doi.org/10.1038/s41586-022-05120-2 Releva

Requirements as to the educational background of candidates that would be suitable for the project
Due to the nature of the project, an undergraduate degree in chemistry or biochemistry is required. The student should have an interest in supramolecular or biophysical chemistry, or artificial cell design and development.

Lead Supervisor: David Buscher, Department of Physics
Co-supervisor: Clark Baker, Department of Physics

Brief summary
The project aims to test a new idea for interferometric wavelength calibration of EPRV spectrographs by building a prototype system and testing it in the laboratory. The new idea uses a broadband light source to illuminate the spectrograph through a Fourier-transform spectrograph (FTS) arrangement. Fourier analysis of the spectra seen for different values of the optical path difference in the FTS will allow high-precision measurement of the spectral response of each pixel.

Importance of the area of research concerned
The detection of ``Earth twins'' – rocky planets orbiting at radii of order 1au around solar-type stars – will be one of the major stepping-stones in our search for life in the Universe. One of the most promising avenues to make these detections is to use a spectrograph to detect the minute changes in the Doppler shift of the spectrum of the parent star caused by the orbiting planet. To extend existing Doppler techniques to the detection of an Earth twin requires extreme wavelength precision – the shifts in wavelength of the stellar spectral lines correspond to much less than a thousandth of the width of a pixel on the detector in the spectrograph. This research addresses the problem of accurately mapping the wavelengths of every pixel in a spectrograph at this level of precision.  

What will the student do?
The student will build a Michelson interferometer in the laboratory and use this to feed light into a test spectrograph. They will develop software in Python to control the interferometer and to analyse the data from the interferometer and the spectrograph. The student will use the results of this analysis to determine how well the system works and recommend future improvements to the system design.

References
Zhao, Lily L., David W. Hogg, Megan Bedell, and Debra A. Fischer. ‘Excalibur: A Nonparametric, Hierarchical Wavelength Calibration Method for a Precision Spectrograph’. The Astronomical Journal 161, no. 2 (January 2021): 80. https://doi.org/10.3847/1538-3881/abd105.

Charsley, Jake M., Richard A. McCracken, Derryck T. Reid, Grzegorz Kowzan, Piotr Maslowski, Ansgar Reiners, and Philipp Huke. ‘Comparison of Astrophysical Laser Frequency Combs with Respect to the Requirements of HIRES’. In Proc. SPIE, 10329:103290Y. International Society for Optics and Photonics, 2017. https://doi.org/10.1117/12.2271846.

Thompson, Samantha J., Didier Queloz, Isabelle Baraffe, Martyn Brake, Andrey Dolgopolov, Martin Fisher, Michel Fleury, et al. ‘HARPS3 for a Roboticized Isaac Newton Telescope’. In Proc. SPIE, 9908:99086F. International Society for Optics and Photonics, 2016. https://doi.org/10.1117/12.2232111.
 

Requirements as to the educational background of candidates that would be suitable for the project
This project requires a degree in Physics or related discipline. It would suit students with a background in optics, computer control of hardware, and data analysis.

Lead Supervisor: Richard Harrison, Department of Earth Sciences
Co-supervisor: Nick Tosca, Department of Earth Sciences

Brief summary
Is strong magnetisation an essential ingredient in the origin of life? A definitive answer to this question would have major implications for the search for life on other planets –narrowing our search to planetary bodies with a stable magnetic field. The CISS effect provides a link between strongly magnetised sediments and homochirality. Sediments are magnetised through a range of natural processes (grain rotation, in-situ grain growth, thermal activation, shock or lightning), most leading to weak or spatially inhomogeneous magnetisation incapable of producing homochirality without additional amplification. Here we will test a range of potential amplification mechanisms that could plausibly operate under early Earth conditions. 

Importance of the area of research concerned
The origin of homochirality, or the selection of one of two mirror-image forms (or enantiomers) of the same molecule, has persisted as a fundamental problem in the origin of life. A recent breakthrough in this field has been made with the discovery of the chiral-induced-spin-selectivity (CISS) effect, which describes a strong enantioselective interaction between ribose-aminooxazoline (RAO) and magnetite surfaces, which induces high-yielding chiral selectivity at a critical point in viable prebiotic reaction networks.1,2 Magnetite may be produced in anoxic alkaline lake settings on the prebiotic Earth and Mars3, but for the CISS effect to operate, the magnetite-rich sediment must be strongly magnetised under the influence of a weak planetary magnetic field and/or be capable of being strongly magnetised by interaction with the RAO molecules. The combination of physical and chemical processes that could have produced sufficiently strongly magnetised sediments are poorly constrained. This project would aim to address this question through a combined experimental and modelling approaches and test the plausibility of the CISS effect as the origin of biological homochirality. 

What will the student do?

The student will study the physical and chemical processes that could have created strong magnetisation in early Earth sediments. This will involve: 

1. Laboratory experiments to grow magnetic minerals (magnetite, greigite) from aqueous solutions under anoxic conditions in the presence of silicate minerals, to mimic the formation of sediments on the early Earth. 
2. Control the experimental conditions to influence the grain size distribution of magnetic minerals, yielding grains in the critical size window (80-100 nm) where theory predicts amplification of remanence could be significant. 
3. Study the interaction of magnetic grains with each other and with the silicate phases (silica, clays) to understand the plausible spatial distributions of magnetic grains in the sediment and the effect of interactions on amplification. 
4. Measure the efficiency of detrital, chemical, and viscous magnetisation processes in these sediments as a function of grain size and grain-grain interactions. 
5. Use micromagnetic modelling and thermal activation theory to predict levels of sedimentary magnetic amplification under plausible early Earth conditions. 

References

• Ozturk, S. F. & Sasselov, D. D. On the origins of life’s homochirality: Inducing enantiomeric excess with spin-polarized electrons. Proc National Acad Sci 119, e2204765119 (2022). 
• Ozturk, S. F., Liu, Z., Sutherland, J. D. & Sasselov, D. D. Origin of biological homochirality by crystallization of an RNA precursor on a magnetic surface. Sci. Adv. 9, eadg8274 (2023). 
• Tosca, N. J., Ahmed, I. A. M., Tutolo, B. M., Ashpitel, A. & Hurowitz, J. A. Magnetite Authigenesis and the Warming of Early Mars. Nat Geosci 11, 635–639 (2018). 

Requirements as to the educational background of candidates that would be suitable for the project
General background in the physical sciences (e.g. physics, chemistry, materials science, Earth sciences, planetary sciences). 

Lead Supervisor: Alex Thom, Chemistry
Co-supervisor: Alex Archibald, Chemistry

Brief summary
There is huge uncertainty in the chemistry that occurred on early-Earth and other planets, and understanding this is one of the keys to understanding the formation of life from prebiotic conditions and assessing whether potential signatures of life seen on other planets are indeed correct and consistent with the chemistry present.

This project creates an automated framework for building reaction networks of relevant species and can generate data not known experimentally through accurate quantum chemical calculations, propagating any uncertainties in this to predicted outcomes., We will apply this to origin-of-life planetary conditions for the first time.

Importance of the area of research concerned
Atmospheric chemistry for present-day Earth contains well-benchmarked reaction networks allowing simulations of many chemical reactions. The environments on early-Earth and other planets are less well characterised, and for many species which do not readily occur on earth, estimates of thermodynamic and kinetic parameters are used, often off by many orders of magnitude.

This research will build a framework for the automatic creation of reaction networks, calculating the relevant quantities to sufficient accuracy, and including estimates of uncertainties, using quantum chemical methods. For gas phase species, these methods give high accuracy.  For condensed-phase species, the lower accuracy of automated methods will be supplemented by state-of-the-art calculations.
We will benchmark this for present-day Earth and experimentally-measured networks used in industrial applications and simulating air quality.

We will then use the networks to simulate early-Earth, Venus, and relevant exo-planet chemistries as these become better established.

What will the student do?
The student will build a python software framework to interface existing quantum chemistry software which calculates thermodynamic and kinetic quantities of relevance.  This framework will also include (and mine) any experimental databases for these quantities, and cross-validate them with computed values.

There are already existing networks, and processes for species generation which can be used to generate reaction networks, but the project may also explore filling-in holes and extending uncharacterised regions of such networks.

Initially the framework will focus on gaseous species, but will be extended to solvated or adsorbed species, where the uncertainties and calculations methods are far from automated, and significant work will be needed in designing interfaces, and collaboration with other specialists in chemistry who work in such areas.

With the generated networks and data the student will investigate and evaluate the plausibility of existing and potential hypotheses for planetary prebiotic chemistries.

References
M. Liu, A. Grinberg Dana, M.S. Johnson, M.J. Goldman, A. Jocher, A.M. Payne, C.A. Grambow, K. Han, N.W. Yee, E.J. Mazeau, K. Blondal, R.H. West, C.F. Goldsmith, W.H. Green. Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation, Journal of Chemical Information and Modeling 61, 2686-2696 (2021).

S. Sharma, A. Arya, R. Cruz and H. J. Cleaves II. Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives, Life 11 1140-1–19 (2021).

A. Pérez-Villa, F. Pietrucci, A. M. Saitta. Prebiotic chemistry and origins of life research with atomistic computer simulations, Phys. Life Rev. 34–35, 105-135 (2020).

Requirements as to the educational background of candidates that would be suitable for the project
Undergraduates in Chemistry, Physics, Earth Sciences, Natural Sciences, and Chemical Engineering would be most suitable, though those some mathematical and programming background from biological sciences could also be suitable.

Lead Supervisor: Helen Williams, Department of Earth Sciences
Co-supervisors: Ross Findlay, Department of Earth Sciences; Mahesh Anand, Department of Physical Sciences, The Open University; Richard Greenwood, Department of Physical Sciences, The Open University; Mike Zolensky, ARES, NASA Johnson Space Centre

Brief summary
Whereas meteorites often contain diverse fragments from the same meteorite group, it is rare for meteorites to contain material belonging to different meteorite groups. Kaidun, a ‘meteorite collection in one stone’ [1. 2], contains many diverse meteorite types including rare aqueously altered, enstatite chondrites and alkaline igneous clasts, preserving a record of collisions between a differentiated planetesimal/planet and the evolution and alteration of primitive inner/outer solar system material. This project will characterise the nature, number and chemistry of the Kaidun lithologies with a view to understanding how interactions between inner and outer solar system primitive asteroids and differentiated planets influenced planetary habitability.

Importance of the area of research concerned
Collisions between planetary precursor meteorites characterised the evolution of our solar system, determining the chemistry and likely habitability of the terrestrial planets. However, direct records of these chaotic cosmic events are rarely preserved, limiting our understanding of their role in the development of habitable terrestrial planets and exoplanets.  

Meteorites provide the only direct record of early solar system events and permit a glimpse of the material central to planetary origins and the delivery of life-essential water/volatiles to planetary bodies. The Kaidun meteorite is an exceptional melange of  altered ordinary, enstatite and carbonaceous chondritic meteorite fragments with rare igneous clasts and preserves a unique record of early solar system mixing and collisions. This project will explore the origins and chemistry of Kaidun’s meteorite clasts, using this meteorite as a natural laboratory to constrain the role that solar system dynamics and planetary collisions played in the creation of habitable terrestrial planets. 

What will the student do?

Using SEM and clean geochemistry facilities at Cambridge and The OU, the student will undertake a petrographic and isotopic characterisation of Kaidun and address the following questions: 

1. What brought Kaidun’s inner and outer solar system lithologies together: is Kaidun a record of the planetary migration events? Can we use Kaidun to constrain the nature and timing of these events and potentially volatile element delivery to terrestrial planets?  
2. No combination of meteorites convincingly reproduces the Earth’s geochemical signatures. Are the clasts in Kaidun identical to known meteorites or are they unique? If the latter, could they be the ‘missing building blocks’ of Earth?  
3. Kaidun’s asteroid must have interacted with a differentiated body, potentially originating from Mars’ moon Phobos. If a link can be established, Phobos (Kaidun) may have captured Martian fragments during impacts. Can these clasts therefore provide insights into early Mars and the evolution of its surface?  

References

[1] Macpherson, G. J., Mittlefehldt, D. W., Lipschutz, M. E., Clayton, R. N., Bullock, E. S., Ivanov, A. V., Mayeda, T. K. & Wang, M.-S. 2009. The Kaidun chondrite breccia: Petrology, oxygen isotopes, and trace element abundances. Geochimica et Cosmochimica Acta, 73, 5493-5511. 
[2] Zolensky, M. & Ivanov, A. 2003. The Kaidun microbreccia meteorite: A harvest from the inner and outer asteroid belt. Geochemistry, 63, 185-246. 
[3] Kuramoto, K., Kawakatsu, Y., Fujimoto, M., Araya, A., Barucci, M. A., Genda, H., Hirata, N., Ikeda, H., Imamura, T. & Helbert, J. 2022. Martian moons exploration MMX: sample return mission to Phobos elucidating formation processes of habitable planets. Earth, Planets and Space, 74, 12. 

Requirements as to the educational background of candidates that would be suitable for the project

This project will suit an enthusiastic and highly motivated individual, preferably with a degree in geoscience, cosmochemistry of planetary science, or someone with relevant laboratory experience.  

The student will be supported and mentored to undertake and disseminate cutting edge research in the internationally competitive field of meteoritics. This project will present an excellent opportunity for the candidate to gain extensive training and analytical skills in the area of extraterrestrial sample science and to work with some of our key collaborators nationally and abroad, including colleagues at The Open University and at the Johnson Space Centre, and position them competitively to participate in preparing for the Mars Moons Explorer mission, scheduled by JAXA to return material from the Martian moon Phobos from 2028 [3].  

Lead Supervisor: Andrew Jardine, Department of Physics
 

Background 

The astrochemical formation of molecules is a highly active field of research and a fundamental step in the development of the chemistry necessary for life in the Universe. A wide range of molecules have now been identified in space [McGuire 2022, ApJS, 259, 30], which typically form through heterogeneous processes on grain surfaces.  Graphitic materials and silicates are relevant, but ice, in the form of amorphous solid water (ASW) is the most important substrate. 

Sophisticated astrochemical network models have been constructed to simulate the molecular formation processes that combine individual atoms then molecules on these surfaces, but such models are typically limited by knowledge of the underlying physical processes on the grains (adsorption, desorption, diffusion) [Cuppen, Astrochemistry, Space Sci. Rev. (2017)].  

Recent and ongoing laboratory based experiments have provided parameters for adsorption and desorption [Hama and  Watanabe, Chem. Rev. 113, 8783 (2013)] but very crude assumptions have been needed to provide the diffusion parameters that are needed in order to make progress.  There is little validation of such assumptions. 

Research Context 

The astrochemistry community has established that new tools are required to provide the diffusion parameters required for progress in this important field [Roadmap for Astrochemical Diffusion Studies, April 2024].  Helium Spin-Echo (HeSE), a technique developed by the Cambridge Surface Physics group, provides the perfect laboratory based technique to supply that information [Tamtögl, Nat. Comms. 12, 3120 (2021)]. To date, the method has been applied to a wide range of technological systems, including the metal surfaces generally associated with heterogeneous catalysis, and a range of 2d materials, but never astrochemically relevant systems. 

The astrochemistry community (notably including Lamberts, Walsh and Ligterink) have recently reached out to PI Jardine in the Cambridge Surface Physics group to address this challenge; the aim of this proposal is to exploit the HeSE technique to address this challenge alongside that community. 

Research Proposal 

The overarching aim of the PhD project is to provide diffusion information relevant to the astrophysical community, which will enable new astrochemical network models to be developed and confidence in existing models to be improved. 

The PhD will focus on gathering experimental data on various systems, starting with simple molecules on graphitic surfaces, then progressing to diffusion on the more complex ASW surface.  Since ASW structures vary, there will be an emphasis on developing methods to grow consistent materials in discussion with other laboratory based ASW experiments, before studying molecular diffusion.  Some instrument development may be required to achieve the low surface temperatures needed.  Similarly, given the level of sophistication of spin-echo data, analysis of the measurements will require molecular dynamics simulations, as well as development of methods for interpreting transport on amorphous surfaces. 

There will be active collaboration with the wider astrochemistry community throughout the project, to optimise experimental design and in order to exploit the resulting measurements.