🔬 Exciting News! I am thrilled to share that our paper, “Topological Linking Determines Elasticity in Limited Valence Networks,” has been published in Nature Materials! 🎉. Read the full paper here

I am excited to announce that our paper on the topological transition of amorphous ices has now been accepted in Physical Review Letters! Huge thanks to Fausto Martelli and Davide Michieletto for an incredible collaboration. What a fantastic way to wrap up the year! Wishing everyone a happy and festive holiday season! 🎉✨

https://doi.org/10.1103/PhysRevLett.133.266102

I had a great time at last week’s Physics of Life PDRA networking event. It was amazing to connect with fellow awardees, gain valuable advice on grant and fellowship applications, and learn about so many exciting scientific projects.

https://www.physicsoflife.org.uk/physics-of-life-pdra-recipient-event.html

The School of Physics and Astronomy (SoPA) at the University of Edinburgh has prepared a promotional video showcasing the research activities conducted within the department. I am incredibly proud and happy to be part of this amazing community, and I’m excited to share that one of my images, featuring work with the TAPLab on DNA nanostars, was selected for the video. Here is the link: https://www.youtube.com/watch?v=b1O0yuwMktU (the image appears at ~0:30).

Thrilled to be participating in this upcoming workshop organised by CECAM: Exploring bio-inspired systems: a synergy between multiscale experimental and computational approaches

Looking at the incredible lineup of speakers, I am sure this is a fantastic opportunity to learn new skills, share ideas, and connect with passionate individuals. Can’t wait to dive in and see what new insights we can gain together.

See you in Vienna.

It was great to be in KU-Leuven and to interact with such wonderful biophysics community. Thanks also for the opportunity to present my work on Biophysical models of DNA elasticity and topology.

The Annual European Rheology Conference 2024 took place in Leeds. I really enjoyed the interaction with researchers applying rheology and theory to understand a broad-range of materials. A key message for me was the need to find a connection between the microscopic structure and macroscopic mechanical properties in several formulations.

I was also happy for the opportunity to present our work on the Rheology of Topologically Active DNA.

I am thrilled to share that I have been awarded one of the PoLNET Post-Doctoral Research Associate Call to study the link between NANOG’s sequence and its function. This will be accomplished by using a combination of MD simulations, Machine Learning and theory.

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

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.

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

I am thrilled to share that my artwork on DNA nanostars has been selected to appear in the front cover of Soft Matter. You can check both, the paper and the artwork in this link

The DNA supercoiling: statistical physics, theoretical models and experiments conference has finished. Thanks to the organizers for the opportunity to present my work on “Transcriptionally driven DNA supercoiling” and to gather together such a wonderful, diverse and interdisciplinary community working in this exciting field.

🎉 Exciting News! 🎉 My first single-authored paper is now live on Soft Matter! Link here 📄🔬 #PublicationAnnouncement #SoftMatter #ResearchMilestone

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.

Thanks to all the wonderful speakers and the early career researchers who registered to the “Topological Soft Matter” workshop we are organizing in Edinburgh.

We look forward to meeting you to a week full of exciting talks, posters and sessions for discussion.

Please don’t forget to check the conference program and booklet here: https://higgs.ph.ed.ac.uk/workshops/topological-soft-matter/

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.

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

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).

I will be presenting our lates results on “Modulation of DNA entanglements by a Nucleoid Associated Protein” in the next Physics of Life meeting, a large-scale conference that will project the excitement of science at the interface between physics and biology. See you in Harrogate!

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)

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.

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.

“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

Very happy to be invited as a speaker in the next ”Topology, Physics and Chemistry of Soft Matter” conference, see you in Trento.

I took this picture just before giving a 6 hours workshop as invited speaker in the Physics department of the Université Paris Cité, as part of the EUTOPIA summer school 2022. I really enjoyed the experience and interaction with students. I also received positive feedback about my tutorials and good ideas for future workshops.

The TABLab is present in the Pint of Science festival 2022. It was great to see the engagement from the public. Well done team!

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

On 21 April I will give a talk as part of the Physics Seminar of the ITESM, please register to receive the zoom link.

¡Asiste al Coloquio de Física: Active DNA Hydrogels!
Impartido por el Dr. Yair Augusto Gutiérrez Fosado.
La cita es mañana 21 de abril a las 11:00 hrs.
https://tinyurl.com/ColoquioFis-Abr21
#YoIngenio

This will be the first time I will participate in the American Physical Society March meeting. I am eager to be part of this event.

APSinvitation

Yesterday we had Donna Strickland in the department with the lecture “From linear Optics to Nonlinear optics to High Intensity Laser Physics”.