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SUMMARY:Multiscale simulation methods and their applications in nucleic ac
 id studies
DTSTART;VALUE=DATE-TIME:20201223T120000Z
DTEND;VALUE=DATE-TIME:20201223T124500Z
DTSTAMP;VALUE=DATE-TIME:20260419T005138Z
UID:indico-contribution-209@indico.bitp.kiev.ua
DESCRIPTION:Speakers: Francesca Mocci (Chemistry and Geological Science De
 partment\, University of Cagliari)\nAfter almost seventy years from the di
 scovery of DNA double helix structure\, we know very much about nucleic ac
 id organization and functions. However\, there are still many structural a
 nd dynamical features - at different spatial and time scales - that have t
 o be understood better. Molecular simulations are essential to understand 
 many properties at the molecular level. With a fast increase in the comput
 er power together with method and software development\, systems over incr
 easing sizes and longer and longer timescales can be simulated. However\, 
 studies of DNA at the atomistic level have a practical maximum size allowi
 ng a few nucleosome core particles\, on the microsecond time scale to be s
 tudied. To reach larger spatial and longer temporal time scales\, necessar
 y when studying many of the biological problems involving DNA (e.g. those 
 connected to DNA flexibility\, or to chromatin folding etc.) all-atom simu
 lations are far too expensive. It is necessary to coarsen the description 
 of the system of interest\, by removing many details non-relevant to the p
 henomenon under investigation [1-4]. In this talk I will present selected 
 coarse-grain (CG) models\, some of which can be applied to the double heli
 x conformation as well as to other nucleic acid structural motifs found in
  the cells\, like DNA quadruplexes [5-6]. Special attention will be given 
 to the methods that can be used to study the counter-ions interactions wit
 h this highly charged poly-ion.\n\nReferences:\n[1] Mocci F\, Laaksonen A 
 (2012). Insight into nucleic acid counterion interactions from inside mole
 cular dynamics simulations is “worth its salt”. Soft Matter\, 8\, 9268
 -9284\n[2] Potoyan DA\, Savelyev A\, Papoian G A (2013) Recent successes i
 n coarse-grained modeling of DNA. WIREs Computational Molecular Science\, 
 3\, 69-8\n[3] Dans PD\, Walther J\, Gómez H\, Orozco M (2016) Multiscale 
 simulation of DNA\, Current Opinion in Structural Biology\, 37\, 29-45\n[4
 ] Sun T\, Mirzoev A\, Minhas V\, Korolev N\, Lyubartsev AP\, Nordenskiöld
  L (2019) \, A multiscale analysis of DNA phase separation: from atomistic
  to mesoscale level\, Nucleic Acids Research\, 47:11\, 5550–5562\,\n[5] 
 Rebič M\, Mocci F\, Lyubartsev AP\, Uličný J\, Laaksonen A (2017) Coars
 e-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Diff
 erent Salt Concentrations ACS Omega 2 (2)\, 386-396\n[6] Rebič M\, Mocci 
 F\, Laaksonen A\, Uličný J (2015) Multiscale simulations of human telome
 ric G-quadruplex DNA. The Journal of Physical Chemistry B 119 (1)\, 105-11
 3\n\nhttps://indico.bitp.kiev.ua/event/7/contributions/209/
LOCATION:Online meeting
URL:https://indico.bitp.kiev.ua/event/7/contributions/209/
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