Biological physics

Research within life sciences includes experimental and theoretical investigations.

Main domains of research include:

  • Experimental investigations pf characteristic space scales in water solutions of DNA and other (bio)polyelectrolites by means of dielectric spectroscopy.
  • Experimental investigations of complexes of RecA proteins and DNA molecules of characteristic helicoidal symmetry.
  • Protein-DNA and protein-RNA interactions.
  • Theoretical investigations of complexion of proteins and DNA molecules. Especially interesting are RNA viruses as systems with spontaneous self-construction. Investigations of DNA viruses as well, especially regarding the condensed phase of DNA molecule within the virus, depending on the presence of one- or two-valence ions.
  • Protein-protein interactions based on electrostatics of charges on proteins in solutions, and the dependence pH and salinity of solution (Poisson-Boltzmann).

Scientific projects

Center of Excellence for Advanced Materials and Sensing Devices,
Research unit: Science of Graphene and Related 2D Structures

MZOS / EU strukturni fondovi
10.11.2014. - 10.11.2019.
Leader: Marko Kralj
Associates: Damir Aumiler, Ticijana Ban, Antonio Šiber, Nataša Vujičić, Tomislav Vuletić, Borna Pielić, Valentino Jadriško, Iva Šrut Rakić, Ida Delač Marion, Marin Petrović, Borna Radatović, Mihovil Jurdana, Dino Novko, Davor Čapeta, Iva Bogdanović Radović (IRB), Hrvoje Buljan (PMF), Maja Buljan (IRB), Andreja Gajović (IRB), Ivan Halasz (IRB), Predrag Lazić (IRB)
Research areas: Surface physics, Solid state physics, Biological physics, Atomic and molecular physics

 

Publications

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A. Lošdorfer Božič, A. ŠiberElectrostatics-Driven Inflation of Elastic Icosahedral Shells as a Model for Swelling of Viruses
Biophys. J. 115, 822 (2018)
DOI: 10.1016/j.bpj.2018.07.032 20180807

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Marion, Sanjin ; San Martín, Carmen ; Šiber, AntonioRole of Condensing Particles in Polymer Confinement: A Model for Virus-Packed “Minichromosomes”
Biophysical journal, 113 (2017), 8; 1643-1653
DOI: 10.1016/j.bpj.2017.08.035 20170814

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I. Jurić, V. González-Pérez, J. M. Hibberd, G. Edwards, and N. J. BurroughsSize matters for single-cell C4 photosynthesis in Bienertia
J. Exp. Bot. 68 (2), 255-267 (2017)
DOI: 10.1093/jxb/erw374 20170101Download publication

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Roman D. Bulushev, Sanjin Marion, Ekaterina Petrova, Sebastian J. Davis, Sebastian J. Maerkl, and Aleksandra RadenovicSingle Molecule Localization and Discrimination of DNA–Protein Complexes by Controlled Translocation Through Nanocapillaries
Nano Lett. 16 (12), 7882–7890 (2016)
DOI: 10.1021/acs.nanolett.6b04165 20161107

S. Marion, I. Delač Marion, N. Maltar-Strmečki, S. Josef-Golubić, and T. Vuletić, editorsABC of Physics of Life : book of abstracts
(Institut za fiziku, Hrvatsko biofizičko društvo, Zagreb, 2016)
Download publication (PDF - 9.66 MB)

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K. Serec, S. Dolanski Babić, R. Podgornik and S. TomićEffect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study
Nucleic Acid Research 44, 8456-8464 (2016)
DOI: 10.1093/nar/gkw696 20160802

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A. ŠiberShapes of minimal-energy DNA ropes condensed in confinement
Sci. Rep. 6, 29012 (8pp) (2016)
DOI: 10.1038/srep29012 20160701

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R. D. Bulushev, S. Marion, and A. RadenovicRelevance of the Drag Force during Controlled Translocation of a DNA–Protein Complex through a Glass Nanocapillary
Nano Letters 15 (10), 7118-7125 (2015)
DOI: 10.1021/acs.nanolett.5b03264 20150922

Danijel GrgičinDynamics and strucutre of deoxyribonucleic acid salt solutions: influence of counterion valency
Institut za fiziku, 2015
Download publication (PDF - 8.82 MB)

I. Delač Marion, D. Grgičin, K. Salamon, S. Bernstorff, and T. VuletićPolyelectrolyte Composite: Hyaluronic Acid Mixture with DNA
Macromolecules 48 (8), 2686–2696 (2015)
DOI: 10.1021/ma502090x 20150415

A. J. Pérez-Berná, S. Marion, F. Javier Chichón, J. J. Fernández, Dennis, C. Winkler, J. L. Carrascosa, A. C. Steven, A. Šiber, and C. San MartínDistribution of DNA-condensing protein complexes in the adenovirus core
Nucleic Acids Res. 43 (8), 4274-4283 (2015)
DOI: 10.1093/nar/gkv187 20150327

S. Marion and A. ŠiberEjecting phage DNA against cellular turgor pressure
Biophys. J. 107 (8), 1924-1929 (2014)
DOI: 10.1016/j.bpj.2014.09.002 20141021

D. Pelc, S. Marion, M. Požek, and M. BasletićRole of microscopic phase separation in gelation of aqueous gelatin solutions
Soft Matter 10, 348-356 (2014)
DOI: 10.1039/C3SM52542B 20140101

D. Grgičin, S. Dolanski Babić, T. Ivek, S. Tomić, and R. PodgornikEffect of magnesium ions on dielectric relaxation in semidilute DNA aqueous solutions
Phys. Rev. E 88, 052703 (8pp) (2013)
DOI: 10.1103/PhysRevE.88.052703 20131105

M. Popović and A. ŠiberLattice-gas Poisson-Boltzmann approach for sterically asymmetric electrolytes
Phys. Rev. E 88, 022302 (5pp) (2013)
DOI: 10.1103/PhysRevE.88.022302 20130808

S. Tomić, D. Grgičin, T. Vuletić, S. Dolanski Babić, T. Ivek, and R. PodgornikDNA in aqueous solutions with repulsive interactions: structure determined on the basis of dielectric spectroscopy measurements
in Bioinformatics and biological physics: proceedings of the scientific meeting, editor V. Paar (HAZU, Zagreb, 2013), pp. 159-176
Download publication

A. Šiber and P. ZiherlMany-body contact repulsion of deformable disks
Phys. Rev. Lett. 110, 214301 (5pp) (2013)
DOI: 10.1103/PhysRevLett.110.214301 20130524

A. Horvatić, I. Dodig, T. Vuletić, D. Pavoković, Z. Hameršak, A. Butorac, and M. CindrićComparison between enhanced MALDI in-source decay by ammonium persulfate and N- or C-terminal derivatization methods for detailed peptide structure determination
Anal. Chem. 85, 3940-3947 (2013)
DOI: 10.1021/ac303436n 20130312

A. L. Božič, A. Šiber, and R. PodgornikStatistical analysis of sizes and shapes of virus capsids and their resulting elastic properties
J. Biol. Phys. 39, 215-228 (2013)
DOI: 10.1007/s10867-013-9302-3 20130301

Completed scientific projects

NanoporeArray: Ion-beam patterned nanopore arrays in polymer supported 2D materials

Provjera inovativnog koncepta PoC
01.06.2016. - 31.05.2017.
Leader: Marko Kralj
Associates: Tomislav Vuletić, Mihovil Jurdana,  
Research areas: Surface physics, Biological physics

QuartzNano: Senzori za kvarcnu mikrovagu unaprijeđeni na nanoskali

Provjera inovativnog koncepta PoC
01.06.2016. - 31.05.2017.
Leader: Tomislav Vuletić
Associates: Marko Kralj, Borna Pielić,
Research areas: Biological physics, Surface physics

Avidin-biotin bond tuned by cryoprotectants

MZOS
01.01.2014. - 31.12.2015.
Leader: Tomislav Vuletić
Associates: P. Hinterdorfer
Research areas: Biological physics

DNA fragments as polyvalent ions regulate lipid multilayers

MZOS
01.01.2014. - 31.12.2015.
Leader: Tomislav Vuletić
Associates: G. Pabst
Research areas: Biological physics

Confined DNA

UKF
15.10.2013. - 14.10.2015.
Leader: Tomislav Vuletić
Research areas: Biological physics

Protein Assisted DNA Monolayer Assembly

UKF
01.01.2008. - 31.12.2009.
Leader: Tomislav Vuletić
Research areas: Biological physics

Energetskom kompeticijom uvjetovani oblici i strukture nanometarskih sustava

MZOS - 035-0352828-2837
01.01.2007. - 31.12.2014.
Leader: Antonio Šiber
Research areas: Biological physics

IF Ⓒ 2017 Ndoc Deda