The ELISIR program recruits exceptional young talents directly after their Ph.D. to run a small team of scientists pursuing innovative independent research in the Life Sciences.
\r\nFeel free to attend this presentation (in SV 1717 or virtually via the zoom link) !
This summer school, organized by seven PhD students from EPFL and ETH Zurich, brings together leading researchers and postgraduate students. Participants will learn modern mathematical and probabilistic methods for linear algebra through lectures by experts in randomized numerical linear algebra. The program also includes networking opportunities with fellow participants, lecturers, and industry representatives.
\r\n
\r\nThe summer school takes place in a modern hotel in the middle of the historic lakeside town of Murten/Morat. Accommodation, food, and all other costs during the summer school will be covered. All participants are charged a small registration fee.
\r\n
\r\nRegistrations can be made until February 15 and are primarily open to doctoral students from the ETH domain, with limited exceptions for international and master’s students. It is possible to obtain 2 ECTS credits for attending MoRAT.
We are delighted to announce the MRI Research Day 2026, which will take place on June 10, 2026, at the Albert Renold Auditorium, CMU, University of Geneva.
\r\nThis one-day event brings together MRI experts from across the Lemanic region and provides a platform to review ongoing MRI projects, share experiences and challenges, and foster collaboration among physicists, physicians, and neuroscientists.
You can apply to participate and find all the relevant information (speakers, abstracts, program,...) on the event website: https://www.cecam.org/workshop-details/multi-scale-and-multi-purpose-simulations-of-dna-the-importance-of-data-1484.
\r\n
\r\nRegistration is required to attend the full event, take part in the social activities and present a poster at the poster session (if any). However, the EPFL community is welcome to attend specific lectures without registration if the topic is of interest to their research. Do not hesitate to contact the CECAM Event Manager if you have any question.
\r\n
\r\nDescription
\r\n
\r\nDNA is a dramatic example of a multiscale system, where Å-scale details impact the global properties of a meter-long fiber and where femtosecond processes can impact on the entire genome years later. This implies that any theoretical study on DNA should take into consideration the vast variety of space and time scales, making it necessary the adoption of multi-physics approaches, covering the entire range of theoretical methods from quantum chemistry to rough mesoscopic models. Within this scenario the importance of data to bias simulations and as a reference to calibrate low resolution methods (Dans et al. 2017; Neguembor et al. 2022; Schultz et al. 2025).
\r\nLarge efforts have been made to develop accurate low level DFT and semiempirical methods that can be data-providers for a new generation of force-field, as well as integrated in QM/MM packages for an efficient representation of DNA reactivity (Aranda et al. 2019). Atomistic force-field have gained accuracy, showing good ability to reproduce unusual forms of DNA and long segments of DNA in the context of chromatin (Collepardo-Guevara et al. 2015; Genna et al. 2025) and providing very useful data for the calibration of lower level coarse-grained or mesoscopic methods(De Pablo 2011; Farré-Gil et al. 2024) ,which have gained sequence specificity, scalability and computational efficiency, allowing to simulate kilo-to-megabase fragments of DNA. Very remarkable efforts have been made to move up these methods to represent chromatin, which requires the introduction of biases derived from experimental data (MNAseq, chromosome conformation capture, and even static or dynamic pictures obtained by ultra-resolution microscopy, and others (Buitrago et al. 2019; Neguembor et al. 2022; Li and Schlick 2024)). This has opened the possibility to recover dynamic “base-pair” resolution pictures of chromatin and study aspects from local and global chromatin rearrangements to inter-play between effector proteins and nucleosomes, the impact of lesions in chromatin structure, and even the role of phase separation in defining local chromatin arrangements (Joseph et al. 2021; Liu et al. 2025; Park et al. 2025).
\r\nAs the target systems move from the small atomistic detail to the entire chromatin fiber, the community is broken into different sub-communities. This generates a risk of disconnection, which would lead to a waste of effort reformulating solutions to already solved problems, or ignoring the characteristic that a method should have to maintain coherence with more accurate models, or to scale to represent systems of real biological interest. This will be the main objective of this meeting, which will join a variety of sub-communities with a common interest: the DNA.
\r\n
\r\nReferences
\r\n
\r\n[1] J. Aranda, M. Terrazas, H. Gómez, N. Villegas, M. Orozco, Nat. Catal., 2, 544-552 (2019)
\r\n[2] D. Buitrago, L. Codó, R. Illa, P. de Jorge, F. Battistini, O. Flores, G. Bayarri, R. Royo, M. Del Pino, S. Heath, A. Hospital, J. Gelpí, I. Heath, M. Orozco, Nucleic Acids Research, 47, 9511-9523 (2019)
\r\n[3] R. Collepardo-Guevara, G. Portella, M. Vendruscolo, D. Frenkel, T. Schlick, M. Orozco, J. Am. Chem. Soc., 137, 10205-10215 (2015)
\r\n[4] P. Dans, I. Ivani, A. Hospital, G. Portella, C. González, M. Orozco, Nucleic. Acids. Res., gkw1355 (2017)
\r\n[5] J. de Pablo, Annu. Rev. Phys. Chem., 62, 555-574 (2011)
\r\n[6] D. Farré-Gil, J. Arcon, C. Laughton, M. Orozco, Nucleic Acids Research, 52, 6791-6801 (2024)
\r\n[7] V. Genna, G. Portella, A. Sala, M. Terrazas, I. Serrano-Chacón, J. González, N. Villegas, L. Mateo, C. Castellazzi, M. Labrador, A. Aviño, A. Hospital, A. Gandioso, P. Aloy, I. Brun-Heath, C. Gonzalez, R. Eritja, M. Orozco, Nucleic Acids Research, 53, (2025)
\r\n[8] J. Joseph, A. Reinhardt, A. Aguirre, P. Chew, K. Russell, J. Espinosa, A. Garaizar, R. Collepardo-Guevara, Nat. Comput. Sci., 1, 732-743 (2021)
\r\n[9] Z. Li, T. Schlick, Nucleic Acids Research, 52, 583-599 (2023)
\r\n[10] S. Liu, C. Wang, B. Zhang, Biochemistry, 64, 1750-1761 (2025)
\r\n[11] M. Neguembor, J. Arcon, D. Buitrago, R. Lema, J. Walther, X. Garate, L. Martin, P. Romero, J. AlHaj Abed, M. Gut, J. Blanc, M. Lakadamyali, C. Wu, I. Brun Heath, M. Orozco, P. Dans, M. Cosma, Nat. Struct. Mol. Biol., 29, 1011-1023 (2022)
\r\n[12] S. Park, R. Merino-Urteaga, V. Karwacki-Neisius, G. Carrizo, A. Athreya, A. Marin-Gonzalez, N. Benning, J. Park, M. Mitchener, N. Bhanu, B. Garcia, B. Zhang, T. Muir, E. Pearce, T. Ha, Nature, (2025)
\r\n[13] E. Schultz, J. Kaplan, Y. Wu, S. Kyhl, R. Willett, J. de Pablo, WIREs. Comput. Mol. Sci., 15, (2025)
Thesis Directors: Dr. C. Cao, Prof. M. Dal Peraro
\r\nBiotechnology and Bioengineering doctoral program
\r\nThesis Nr. 11784
\r\n
\r\nTo take part in the public defense, please contact directly the speaker