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SUMMARY:Multi-scale and multi-purpose simulations of DNA: the importance o
 f data
DTSTART;VALUE=DATE:20260826
DTSTAMP:20260407T101426Z
UID:5376306182863a7af09c7d385ddc404af06d2b1e3d7353acd9387d3f
CATEGORIES:Conferences - Seminars
DESCRIPTION:You can apply to participate and find all the relevant informa
 tion (speakers\, abstracts\, program\,...) on the event website: https://
 www.cecam.org/workshop-details/multi-scale-and-multi-purpose-simulations-o
 f-dna-the-importance-of-data-1484.\n\nRegistration is required to attend t
 he 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 in
 terest to their research. Do not hesitate to contact the CECAM Event Mana
 ger if you have any question.\n\nDescription\n\nDNA is a dramatic example
  of a multiscale system\, where Å-scale details impact the global propert
 ies of a meter-long fiber and where femtosecond processes can impact on th
 e entire genome years later. This implies that any theoretical study on DN
 A 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 m
 esoscopic models. Within this scenario the importance of data to bias simu
 lations and as a reference to calibrate low resolution methods (Dans et al
 . 2017\; Neguembor et al. 2022\; Schultz et al. 2025).\nLarge efforts have
  been made to develop accurate low level DFT and semiempirical methods tha
 t can be data-providers for a new generation of force-field\, as well as i
 ntegrated in QM/MM packages for an efficient representation of DNA reactiv
 ity (Aranda et al. 2019). Atomistic force-field have gained accuracy\, sho
 wing good ability to reproduce unusual forms of DNA and long segments of D
 NA in the context of chromatin (Collepardo-Guevara et al. 2015\; Genna et 
 al. 2025) and providing very useful data for the calibration of lower leve
 l coarse-grained or mesoscopic methods(De Pablo 2011\; Farré-Gil et al. 2
 024) \,which have gained sequence specificity\, scalability and computatio
 nal efficiency\, allowing to simulate kilo-to-megabase fragments of DNA. V
 ery remarkable efforts have been made to move up these methods to represen
 t chromatin\, which requires the introduction of biases derived from exper
 imental data (MNAseq\, chromosome conformation capture\, and even static o
 r dynamic pictures obtained by ultra-resolution microscopy\, and others (B
 uitrago et al. 2019\; Neguembor et al. 2022\; Li and Schlick 2024)). This 
 has opened the possibility to recover dynamic “base-pair” resolution p
 ictures of chromatin and study aspects from local and global chromatin rea
 rrangements to inter-play between effector proteins and nucleosomes\, the 
 impact of lesions in chromatin structure\, and even the role of phase sepa
 ration in defining local chromatin arrangements (Joseph et al. 2021\; Liu 
 et al. 2025\; Park et al. 2025).\nAs the target systems move from the smal
 l 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 s
 olved 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 t
 his meeting\, which will join a variety of sub-communities with a common i
 nterest: the DNA.\n\nReferences\n\n[1] J. Aranda\, M. Terrazas\, H. Gómez
 \, N. Villegas\, M. Orozco\, Nat. Catal.\, 2\, 544-552 (2019)\n[2] D. Bui
 trago\, 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)\n[3]
  R. Collepardo-Guevara\, G. Portella\, M. Vendruscolo\, D. Frenkel\, T. Sc
 hlick\, M. Orozco\, J. Am. Chem. Soc.\, 137\, 10205-10215 (2015)\n[4] P. 
 Dans\, I. Ivani\, A. Hospital\, G. Portella\, C. González\, M. Orozco\, N
 ucleic. Acids. Res.\, gkw1355 (2017)\n[5] J. de Pablo\, Annu. Rev. Phys. C
 hem.\, 62\, 555-574 (2011)\n[6] D. Farré-Gil\, J. Arcon\, C. Laughton\, 
 M. Orozco\, Nucleic Acids Research\, 52\, 6791-6801 (2024)\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. H
 ospital\, A. Gandioso\, P. Aloy\, I. Brun-Heath\, C. Gonzalez\, R. Eritja\
 , M. Orozco\, Nucleic Acids Research\, 53\, (2025)\n[8] J. Joseph\, A. Re
 inhardt\, A. Aguirre\, P. Chew\, K. Russell\, J. Espinosa\, A. Garaizar\, 
 R. Collepardo-Guevara\, Nat. Comput. Sci.\, 1\, 732-743 (2021)\n[9] Z. Li
 \, T. Schlick\, Nucleic Acids Research\, 52\, 583-599 (2023)\n[10] S. Liu
 \, C. Wang\, B. Zhang\, Biochemistry\, 64\, 1750-1761 (2025)\n[11] M. Neg
 uembor\, J. Arcon\, D. Buitrago\, R. Lema\, J. Walther\, X. Garate\, L. Ma
 rtin\, 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. B
 iol.\, 29\, 1011-1023 (2022)\n[12] S. Park\, R. Merino-Urteaga\, V. Karwa
 cki-Neisius\, G. Carrizo\, A. Athreya\, A. Marin-Gonzalez\, N. Benning\, J
 . Park\, M. Mitchener\, N. Bhanu\, B. Garcia\, B. Zhang\, T. Muir\, E. Pea
 rce\, T. Ha\, Nature\, (2025)\n[13] E. Schultz\, J. Kaplan\, Y. Wu\, S. Ky
 hl\, R. Willett\, J. de Pablo\, WIREs. Comput. Mol. Sci.\, 15\, (2025)
LOCATION:BCH 2103 https://plan.epfl.ch/?room==BCH%202103
STATUS:CONFIRMED
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