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Category: Posts

GEOTOP-A seminar

I am excited to go back to Mexico on January next year, to be part of this amazing event (GEOTOP-A seminar) and to talk about our most recent project on “Topological Elasticity”.

Looking forward to visiting Merida, having great food and to interact with this great community.

Link to the event: https://seminargeotop-a.com/merida24

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Advanced core-to-core network for the physics of self-organizing active matter

I am now in Kyoto for the first core-to-core network. Prof. Masao Doi gave a talk about the current efforts to understand the swelling of gels. I feel so lucky to have the opportunity to interact with such amazing scientists. Tomorrow, I will be talking about a recent project in which we use Restriction Enzymes to change the viscoelastic properties of DNA hydrogels. If interest, the full program is available here.

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International Soft Matter Conference ISMC2023

Very happy to have participated as chair in one of the sessions and also to have been selected as a speaker in this amazing event. It was a pleasure to talk about our latest pre-print “Topological Elasticity in Physical Gels with Limited Valence“, and also to hear all the interesting research that is currently developed in the soft matter field. Looking forward to participate in the ISMC next year!

You can take a look at the program of the event here

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End of workshop

The Topological Soft Matter has concluded. It was an incredible experience interacting with exceptional scientists from various fields such as physics, chemistry, mathematics, and biology. The discussions and perspectives shared during the conference were insightful and inspiring. I am honored to have organized this event (alongside Simon Weir and Valerio Sorichetti). Also, I am excited about the possibilities of fruitful collaborations, training schools, networking, and groundbreaking scientific research that may arise from this event.

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Physics of Life Conference 2023

The Physics of Life conference took place last week in Harrogate, UK. It was amazing to meet a lot of people in the community working on a wide range of interesting topics.
I presented a poster on our latest work “Modulation of DNA entanglements by a Nucleoid Associated Protein” that received positive feedback. Also, I enjoyed listening the keynote speakers. There were a lot of opportunities for networking, that I hope turn into future collaborations.

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Outreach preparation

We are preparing a Virtual Reality activity for the next Edinburgh Science Festival. Work spearheaded by an impressive MPhys student Kira 🙌. Hope to see you at the National Museum of Scotland this Wednesday 5 April. More information here

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AI, Engineering Biology & Beyond

This week I attended to the Turing workshop on AI, Engineering Biology & Beyond. It was very interesting to find how these fields have seen tremendous growth in recent years, with AI being increasingly adopted across every stage of the Engineering Biology design cycle and for a growing number of biological design tasks.

Alexander Pritzel from Deepmind (the company behind alpha-fold) was there.

Natalio Krasnogor explained their currrent efforts to create a data structure using DNA for data storage and computational purposes.

Cleo Kontoravdi mentioned how AI can be used to have a better control on processes for bioreactors to increase their yield.

… And many other interesting ideas. It seems to me that this is the future in the field and Edinburgh is one of the best places in the world to be part of this change (with plenty of opportunities for Theoretical/Computational Physicists).

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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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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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Impact talks

Recently, there have been a series of talks about ”impact” in the ICMCS institute in which I work. The idea is that researchers who have successfully translated their research into something useful for society, explain to collaborators how was their process to accomplish this.
In the most recent talk, Wilson Poon (a top physicist in soft condensed matter) explained how was his first approach with companies and also his journey to create the Edinburgh Complex Fluids Partnership https://www.edinburghcomplexfluids.com
It was really inspiring!!
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DNA as clay

This is just beautiful

“One of the most surprising (and thought provoking) feats of molecular engineering in this burgeoning area, is the construction by Nadrian Seeman and his coworkers at New York University, of giant (relative to most molecules), little (on the scale of macroscopic matter) stick figures, polyhedra and knots out of DNA.

Out of DNA? The idea seems wild -DNA is not your typical synthetic master sculptor’s clay. The notion also seems transgressive of natural order- to build geometric objects of no intrinsic value from genetic material. Let me face the second concern first, even before I show you the principles of this beautiful sculpture.

The nucleic-acid “system” that operates in terrestrial life is optimized (through evolution) chemistry incarnate. Why not use it? Not to make genetic manipulations of human DNA, which quite justifiably provokes ethical questions. But to allow human beings to sculpt something new, perhaps beautiful, perhaps useful, certainly unnatural. As beautiful and unnatural as a Schubert song or the American Constitution.”

DNA as Clay,
By Roald Hoffmann.

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Size Matters

“Although is a common public perception that the frontier of understanding in physical science lies at ever-smaller-scales, the truth is that barriers to our understanding of the material world tend to lie in the other direction: in the problem of scaling up”

Size Matters,
by Phillip Ball
Link to the article

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New paper

Our new work is now out in Nucleic Acids Research. We compared different mechanisms to find the most efficient way in which type2-topoisomerase, an enzyme that “cuts” and “reseals” double-stranded DNA, finds and resolves DNA knots. Read more in NAR

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Kinetoplast workshop

Olympic gels are “mythological beasts” in soft matter and material science. Hypothesised by P.G. de Gennes in the 1980s by topologically interlinking ring-shaped polymers, they are extremely challenging to synthesise chemically. Recently, physicists realised that Olympic gels existed in nature for millions of years.
Discovered in the 1970s by a biologist, a “kinetoplast DNA” is the mitochondrial genome of blood sucking parasites called Trypanosomes. They carry deadly diseases with important health and economic consequences especially in tropical and subtropical regions of Africa and South America. Beyond their impact on human health, Trypanosomes are fascinating unicellular organisms because of their complex life cycle and their unique mitochondrial genome which consists of covalently closed DNA rings forming a 2D flat sheet of interlinked rings and curiously resembling a medieval chainmail. How this unique structure came into existence is a question that has been puzzling biologists for decades but attracted the attention of bio and soft matter physics only in the last 5 years.
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