High density DNA arrays: models, theories and multiscale simulations

Location : National Institute of Chemistry, Ljubljana, Slovenia
July 24, 2019 – July 26, 2019

Organizing Committee:
Matej Praprotnik, National Institute of Chemistry, Ljubljana, Slovenia
Miha Ravnik, Faculty of Mathematics and Physics, University of Ljubljana, Slovenia
Primož Ziherl, Faculty of Mathematics and Physics, University of Ljubljana, and Jožef Stefan Institute, Ljubljana, Slovenia
Rudolf Podgornik, University of Chinese Academy of Sciences, Beijing, China

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

Having IUPAP Conference Endorsement, this CECAM workshop is a satellite meeting of the Joint 12th EBSA 10th ICBP-IUPAP Biophysics Congress, Madrid, Spain. We therefore subscribe to the statement on free circulation of scientists in addition to CECAM’s own policies.


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).


Natasa Adzic (invited speaker) (Faculty of Physics, University of Vienna)
Clemens Jochum (invited speaker) (TU Wien)


Amélie Leforestier (invited speaker) (Universite Paris-Sud)


Christoph Cremer (invited speaker) (Institute of Molecular Biology (IMB))
Christian Holm (invited speaker) (Institute for Computational Physics, University of Stuttgart)
Kurt Kremer (invited speaker) (Max Planck Institut for Polymer Research, Mainz)
Stanard Mebwe Pachong (Max Planck Institute for Polymer Sciences)


Tommaso Bellini (invited speaker) (University of Milan)
Achille Giacometti (invited speaker) (Dip. Chimica Fisica, Univ. Venezia)
Cristian Micheletti (invited speaker) (International School for Advanced Studies (SISSA), Trieste)
Angelo Rosa (invited speaker) (International School for Advanced Studies (SISSA), Trieste)

The Netherlands

Bart Bruininks (University of Groningen)


Nikolay Korolev (School of Biological Sciences, Nanyang Technological University)


Irena Drevenšek Olenik (invited speaker) (Faculty of Mathematics and Physics, University of Ljubljana)
Matej Kanduč (Jozef Stefan Institute, Ljubljana)
Anze Losdorfer Bozic (Jozef Stefan Institute)
Franci Merzel (invited speaker) (National Institute of Chemistry)
Petra Papež (National Institute of Chemistry, Ljubljana)
Aleksandar Popadić (National Institute of Chemistry, Ljubljana)
Lea Spindler (University of Maribor, Slovenia)

Jurij Sablić (invited speaker) (National Institute of Chemistry)
Daniel Svenšek (invited speaker) (Faculty of Mathematics and Physics, University of Ljubljana)


Salvatore Assenza (Universidad Autónoma de Madrid)


Alexander Lyubartsev (invited speaker) (Stockholm University)

United Kingdom

Jure Dobnikar (invited speaker) (Institute of Physics, Chinese Academy of Sciences and University of Cambridge, Department of Chemistry)
Jonathan Doye (invited speaker) (University of Oxford)
Alexei Kornyshev (invited speaker) (Imperial College London)


Aleksei Aksimentiev (invited speaker) (University of Illinois at Urbana-Champaign)

Day 1 (Wednesday, July 24):

8:00-8:45: registration

8:45-9:00: opening

9:00-9:45: Aleksei Aksimentiev

9:45-10:30: Jonathan Doye

10:30-11:00: Coffee break

11:00-11:45: Christoph Cremer

11:45-12:30: Jurij Sablić

12:30-14:00: Lunch

14:00-14:45: Alexander Lyubartsev

14:45-15:30: Nikolay Korolev

15:30-16:00: Coffee break

16:00-16:45: Round table

16:45-17:30: Amélie Leforestier

17:30-18:15: Bart Bruininks

18:15-18:45: Salvatore Assenza

Day 2 (Thursday, July 25):

9:00-9:45: Kurt Kremer

9:45-10:30: Achille Giacometti

10:30-11:00: Coffee break

11:00-11:45: Tommaso Bellini

11:45-12:30: Jure Dobnikar

12:30-14:00: Lunch

14:00-14:45: Round table

14:45-15:30: Christian Holm

15:30-16:15: Cristian Micheletti

16:15-16:30: Coffee break

16:30-17:15: Daniel Svenšek

17:15 – Dinner (Kobjeglava, Štanjel by bus)

Day 3 (Friday, July 26)

9:00-9:45: Alexei Kornyshev

9:45-10:30: Angelo Rosa

10:30-11:00: Coffee break

11:00-11:45: Irena Drevenšek Olenik

11:45-12:30: Franci Merzel

12:30-14:00: Lunch

14:00-14:45: Round table

14:45-15:30: Natasa Adzic

15:30-16:15: Clemens Jochum

16:15-16:30: Coffee break

16:30-17:00: S.M. Pachong

17:00-17:30: Matej Kanduc

17:30-18:00: Open discussion and Conclusion

Christoph Cremer – Super Resolution Microscopy of DNA packaging in Mammalian Cell Nuclei

Tommaso Bellini – DNA without DNA: Watson-Crick Selectivity Controls the self-Assembly of Mononucleotides

Alexander Lyubartsev – Multiscale simulations of DNA aggregation by multivalent ions

Angelo Rosa – From Chromosome Territories to Ring Polymers: Physical Properties of Untangled Polymer Melts

Jonathan Doye –  Lyotropic cholesteric phases of DNA and its assemblies

Jure Dobnikar – Spontaneous Domain Formation in Spherically-Confined Elastic Filaments

Cristian Micheletti – Effect of knots during viral DNA packaging and ejection

Achille Giacometti – Toward controlled Self-assembly of peptides

A.A. Kornyshev – Homology recognition without proteins

Natasa Adzic – DNA-based dendrimers: from a single molecule to the dense solution description

Amélie Leforestier – Nucleosome conformational variability in interphase nuclei and in solution explored by cryo-electron microscopy and tomography of vitreous sections

Irena Drevensek-Olenik – “Genetics” in two dimensions: DNA base pairing in thin surface films

Franci Merzel – Atomistic MD simulations as a tool to elucidate mechanical properties of DNA/RNA systems

Christian Holm – How to Model DNA Translocation through Nanopores – A Multiscale Simulational Exploration

Daniel Svenšek – Density–nematic coupling in isotropic linear polymers: acoustic and osmotic birefringence

Nikolay Korolev – Analysis structures and forces defining chromatin condensation

Matej Kanduč – Aqueous Nanoclusters Govern Ion Partitioning in Dense Thermoresponsive Polymer Membranes

Kurt Kremer – Polymer Globules in Bulk and in Confinement

Clemens Jochum – Free energy landscapes for dendrimer-like DNAs via neural networks

Bart Bruininks – Genetic outbreak from the endosome: a molecular perspective on gene therapy

S.M. Pachong – Dynamics and organization of cyclic polymers melt in a connement

Jurij Sablić – Open Boundary Molecular Dynamics of Star-Polymer Melt and DNA in Salt Solution

Aksimentiev, Aleksei – Modeling high density DNA arrays: Mission accomplished!

Salvatore Assenza – Multiscale simulations of double-stranded DNA with sequence-dependent mechanical and conformational properties