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Projects / Programmes source: ARIS

Theory of the nematic nanodroplet and ordering of DNA, encapsidated in simple viruses

Research activity

Code Science Field Subfield
1.02.07  Natural sciences and mathematics  Physics  Biophysics 

Code Science Field
B002  Biomedical sciences  Biophysics 

Code Science Field
1.03  Natural Sciences  Physical sciences 
Keywords
polymer nematic, DNA, nanodroplet, virus, ordering and density variation, defects
Evaluation (rules)
source: COBISS
Researchers (7)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  08589  PhD Rudolf Podgornik  Physics  Head  2011 - 2014  705 
2.  32151  PhD Dalija Povše Jesenek  Mathematics  Researcher  2014  33 
3.  32154  PhD Anže Rapoš Božič  Physics  Junior researcher  2011 - 2013  65 
4.  17046  PhD Gregor Skačej  Physics  Researcher  2011 - 2014  110 
5.  19136  PhD Daniel Svenšek  Physics  Researcher  2011 - 2014  203 
6.  18142  PhD Andreja Šarlah  Physics  Researcher  2011 - 2012  97 
7.  21609  PhD Andrej Vilfan  Physics  Researcher  2011 - 2014  249 
Organisations (2)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0106  Jožef Stefan Institute  Ljubljana  5051606000  90,976 
2.  1554  University of Ljubljana, Faculty of Mathematics and Physics  Ljubljana  1627007  34,275 
Abstract
In the proposed project we investigate the packing of a nematic liquid crystal polymer into a rigid enclosure. The motivation clearly arises from packing of DNA into viral capsids. Packing of DNA within simple viruses has recently attracted a lot of attention from the physics community since it appears that many if not all processes connected with the bacteriophage DNA injection are governed by biologically unspecific physical mechanisms. The virus capsid, normally a decorated icosahedron, can be well represented by a hard sphere. In our studies the DNA is treated as a nematic polymer in a continuum description including orientation-elastic, phase ordering, and density-coupling effects characteristic to the polymer nematic, as a contrast to complementary molecular dynamics or density functional descriptions. We develop a 3D PDE solver for hydrodynamics of complex fluids and apply it to the dynamics of DNA packing and other hot systems, including active nematics and micro/nanofluidics.
Significance for science
We have proposed a change in perspective and analyzed the confined nematic polymer such as DNA in terms of a polymer nematic ordering framework by writing down a Landau-de Gennes-type confined nematic polymer free energy. Motivated primarily by the recent experiments on condensed DNA states inside bacteriophage capsids, we have generalized the confined nematic polymer analysis in more aspects, in particular by explicitly describing the condensation transition. As a result, the condensed nematic polymer configuration builds up ab initio (no implied Ansatz) from a completely random initial state (pure thermal noise). We have derived an important new tensorial conservation law for nematic polymers, coupling the nematic order tensor gradients with density variations and complementing the already established vectorial polymer current conservation. It must be stressed that it is similarly important and fundamental for the macroscopic description of ordered polymers as the continuity equation is for fluid dynamics. Therefore we expect that it will have a frontier-breaking impact on the continuum description of ordered polymers in general. Up till now all macroscopic calculations of ordered structures have implemented the vectorial constraint. We have shown, however, that under certain conditions it should be substituted by the new tensorial constraint. The new tensorial conservation law thus represents a stark deviation from the previously considered constraints implied by the polymeric nematogens and will fundamentally change our perspective on the relation between simple and polymeric nematogens. It will by necessity lead to a reconsideration of some of the existing results on polymer nematics, where this new constraint has not been adequately taken into account. The introduction of the concept of a dynamic preferred direction represents an important change in view upon macroscopic description of active systems. It detours from the current description based on static ordering with added activity, enabling macroscopic description of the dynamics of orientationally ordered systems that possess a preferred direction only dynamically, macroscopically or even microscopically. Within the hydrodynamic and nonequilibrium thermodynamic framework it brings about couplings that are not allowed by symmetry in the case of the static preferred direction, while at the same time introducing a direct coupling of orientational ordering and transport.
Significance for the country
Within this project we have developed models, theoretical concepts, macroscopic theories, and computational methods for the description of orientational ordering in complex fluids, also in relation with dynamics and hydrodynamics. In these endeavours we collaborate with field-leading researchers and groups worldwide (Amherst, Bayreuth, Mainz, Paris, Bordeaux, Lund, Tel Aviv, Teheran, Erevan ...). Through these collaborations we preserve the fluidity and contact of Slovenian science with the cutting edge international research. We also collaborate with several groups in Slovenia, e.g., with the institutes IJS, KI, several faculties of all national universities. The developed concepts are also transferred to employment for pedagogical purposes and popularization of the scientific field. The project group members have also mentored/comentored several doctoral dissertations, master and diploma theses. The results of our research are published in top international scientific journals and presented at several international and domestic scientific conferences. Therewith we contribute to the renownedness of Slovenia and the preservation and promotion of the reputation of Slovenian science.
Most important scientific results Annual report 2011, 2012, 2013, final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Annual report 2011, 2012, 2013, final report, complete report on dLib.si
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