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Workshops

High density DNA arrays: models, theories and multiscale simulations

July 24, 2019 to July 26, 2019
Location : Ljubljana, Slovenia

Organisers

  • Matej Praprotnik (National Institute of Chemistry, Ljubljana, Slovenia)
  • Miha Ravnik (University of Ljubljana, Slovenia)
  • Primoz Ziherl (University of Ljubljana, Slovenia)
  • Rudolf Podgornik (University of Ljubljana, Slovenia)

Supports

   CECAM

Description

Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them, as affected also by the length of the DNA strands or fragments. While we have some underanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remain less well understood.
 
Since at high DNA densities, i.e., small interaxial spacings, one can neglect neither the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent and then mesosopic level, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale approaches coupling atomistic, mesoscopic, and macroscopic levels of detail therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior.
 
With the proposed workshop, we wish to address the simulation approaches to the dense DNA arrays with different local packing symmetries, the solvent structural order, and counterion types. The aim of the meeting is to discuss numerical and theoretical methods and models at different length scales applicable to such systems to analyze the osmotic equation of state, to identify the most important contributions to the DNA-DNA interactions at high DNA densities, to determine possible liquid crystalline ordering profiles and explore means for controlling the DNA packing and ordering. In an unrestrained atmosphere of an interdisciplinary workshop including physicists, chemists, and biologists these goals may be reached to mutual benefit of the participants as well as indirectly of the scientific community.
 
Overall, there is a growing need for a clear jump forward by the community in the methodology and approaches capable of addressing dense DNA arrays, and we are convinced that the proposed CECAM workshop could be notable contribution in this direction, opening a focused but broadly relevant forum for novel discussions and advances in these issues.
        
The objective of the workshop is to address the following main open issues:

  • multiscale methods coupling different models at various length scales
  • performing open grand-canonical molecular simulations that exchange energy, momentum, and matter with the external environment
  • determination of phase transitions between DNA subphases beyond invoking the general Lindemann criterion, using enhanced sampling techniques
  • determination of DNA to surface interactions (surface anchoring) in view of orientational and positional order of DNA
  • identification of material regimes and system parameters for use of dense DNA materials as advanced macroscopic materials, such as in bio-photonics

References

Ten selected references:

1.T. Bellini, R. Cerbino, and G. Zanchetta, Top. Curr. Chem. 318, 225 (2011).
2. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
3. J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
4. A. A. Kornyshev, D. J. Lee, S. Leikin, and A. Wynveen, Rev. Mod. Phys. 79, 943 (2007).
5. S. Yasar, J. Schimelman, M. A. Aksoyoglu, N. Steinmetz, R. French, V. Parsegian, and R. Podgornik, Sci. Rep. 6, 27079 (2016).
6. J. Yoo and A. Aksimentiev, Nucl. Acids Res. 44, 2036 (2016).
7. D. Frenkel and B. Smit, Understanding molecular simulation (2nd edition), Academic Press (2002).
8. R. Podgornik, J. Zavadlav, and M. Praprotnik, Computation 6, 3 (2018).
9. L. Delle Site and M. Praprotnik, Phys. Rep. 693, 1 (2017).
10. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002).