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Month: February 2023

27/Feb/2023 Dominique Laniel

Producing the Ultimate High Energy Density Material

Nitrogen is a truly unique element. As a diatomic molecule, N2, is extremely stable and features the strongest homoatomic bond. However, under the application of extreme pressures and temperatures, the N2 molecule breaks apart and nitrogen transforms into a 3D polymeric solid called cubic gauche polymeric nitrogen (cg-N). This solid, comprised solely of single-bonded nitrogen atoms, is the ultimate high energy density material. It can store and release about 10x more energy than the best compounds and is 100% environmentally friendly. A small problem remains: cg-N cannot be recovered to ambient conditions.

In this talk, we will explore a variety of experimental high-pressure high-temperature paths to produce alternatives to cg-N. An unexpectedly large zoology of nitrogen species is discovered, with many exotic and exciting properties, including materials highly energetic and fully recoverable to ambient conditions.

Room 2511 JCMB

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2023/Feb/20 Job Thijssen

Interfacial rheology – measuring mechanical properties of complex-liquid interfaces

In this presentation, I will introduce colloidal, micron-sized particles at liquid interfaces. These are interesting 2D model systems, but they are also interesting for (potential) applications e.g. particle-stabilized aka Pickering emulsions and bijels (bicontinuous Pickering emulsions). The mechanical properties of the particle-laden interfaces are challenging to measure, but they are important, for example to explain Pickering-emulsion stability. I will summarize some of our past and recent work on measuring and interpreting the mechanical properties of particle-laden liquid interfaces, including our recent development of ‘contactless’ interfacial rheology.

Today at 4:00 pm, back in JCMB room 2511.

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2023/Feb/13 Pamela Knoll

Biomimetic crystallization of biomorphs and chemical gardens: Understanding their formation and studying their self-motion

Abiotic crystallization is typically described by classical models to form geometric shapes with flat faces, sharp edges, and well defined angles. This is in stark contrast to crystallization routes used by living systems which instead grows smoothly curved shapes such as teeth, bone, and nacre. Such morphological distinctions have been applied to determine the biogenicity of structures found in ancient rocks. However, laboratory experiments in far-from-equilibrium systems are able to precipitate similar curvilinear morphologies previously only prescribed to living organisms thus blurring the line between structures derived from biotic and abiotic origins. The first example I will discuss is the crystallization of metal carbonate and silica microstructures known as “biomorphs”. They are composed of thousands of coaligned nanorods that self-organize into larger life-like shapes such as leaf-like sheets, helices, funnels, and flowers. At the nanoscale, the growing crystallization front forms from the addition of smaller nanodot building units that merge into the elongated rod shape. At the microscale, the pseudo two-dimensional sheet shape can be simulated using reaction-diffusion equations. Finally, the hierarchical ordering is extended into the centimeter scale with the merging of neighbouring biomorphs at the air-solution interface. The second example is chemical gardens. Formed from steep chemical gradients between a metal salt and a solution of silicate, the final result is hollow tubes which resemble filaments found in many geological settings. This quick and easy production process for generating tubes can be exploited by controlling the composition of the final material to create self-moving chemical gardens.

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Topological Soft Matter Workshop

We would like to invite you to the interdisciplinary workshop “Topological Soft Matter”, where we aim to bring together scientists from different fields working on soft materials in which topology is key. We want to offer the occasion to discuss and identify the main challenges in this exciting emerging field, to facilitate networking and to create fertile ground for new collaborations.

When? 10-12 May 2023
Where? Higgs Centre for Theoretical Physics, School of Physics and Astronomy, University of Edinburgh (UK).
Website: https://higgs.ph.ed.ac.uk/workshops/topological-soft-matter

All participants are encouraged to contribute with a poster.
The deadline for the poster abstract submission is 10 April 2023 at 13:00 GMT.
Do not hesitate to contact us for further information, and to share this announcement with colleagues, and in particular junior researchers who might be interested.
We are looking forward to your participation,
The Organizers
Yair Fosado (University of Edinburgh, UK)
Valerio Sorichetti (Institute of Science and Technology, Austria)
Simon Weir (University of Edinburgh, UK)

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2023/Feb/06 Chris Brackley

“Polymer physics of cancer genomes”

While every cell in our bodies contains the same genome, different sets of genes are active in different types of cell, and the “switching on and off” of specific genes must be tightly controlled as cells develop. Gene regulation is tightly related to the spatial organisation of the chromosomes within the cell nucleus. A number of physical mechanisms through which this organisation is controlled have been identified, and polymer physics models have proved extremely useful for understanding these. I will present recent work in which polymer models were used to understand genome rearrangements in cancer. There are several methods which the cell employs to repair the genome should the DNA get broken, however these sometimes do not work correctly, and genome rearrangements can arise. For example, two different broken chromosomes could get joined together; this changes the spatial organisation, disrupts gene regulation, and can give rise to disease. Our polymer simulations were able to predict the changes in gene expression which result from genome rearrangements commonly found in B-cell cancers, shedding light on this poorly understood process. The results also allowed us to identify specific sites on the DNA which drive oncogene overexpression after the rearrangement. We are now performing genome editing experiments which target these sites with a view to reversing the over-expression; this will provide new understanding which could eventually lead to new therapies.

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New papers

I am thrilled to share that two of our papers have been accepted for publication in Physical Review Letters on the same day. What a happy coincidence.

The first one marks the first paper in my career in which we combine simulations, theory and experiments to shed some light on the biophysics of cells. All living cells have a problem, the environment where their DNA is stored is typically very crowded and entangled. In order to execute essential tasks such as gene expression and cell division, cells require DNA to be dynamic and to flow. Our findings suggest, for the first time, that bacterial proteins involved in DNA packaging may act as “rheology modifiers” in living cells and modulate the viscosity of their surroundings. Read more in PRL.

The second paper is part of a project that I started by the end of my postdoc in Japan (~2020) in which we tackle a  fundamental problem in DNA elasticity. Existing theories of suggest that the bending and twisting persistence lengths of DNA, two quantities related to the DNA stiffness, are constant (under constant salt, PH and temperature conditions). This was supported by single-molecule experiments performed with long DNA molecules. However, recent experiments have reported the high flexibility of short DNA fragments characterised with a short persistence length whose origin and relation to the existing models have been under active debate. In this work we provide a systematic description of the link between models of DNA elasticity at different length scales that helps to elucidate the length dependence elasticity of DNA, and with this, how bulk elastic properties emerge from base-pair fluctuations. Read more in PRL.

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