Projects / Programmes source: ARIS

Experimental biophysics of complex systems

Research activity

Code Science Field Subfield
1.02.00  Natural sciences and mathematics  Physics   

Code Science Field
B260  Biomedical sciences  Hydrobiology, marine biology, aquatic ecology, limnology 
Biophysics, membranes, cells, tissues, magnetic resonance, spin labels, spin traps, antioxydative processes, spectral simulation, liposomes, nanoparticles, oxymetry, diffusion, spin echo, porous heterogeneous structures, flow, chromatography, agro technology, catalyze
Evaluation (rules)
source: COBISS
Researchers (21)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  23566  PhD Zrinka Abramović  Physics  Junior researcher  2004 - 2007  42 
2.  20208  PhD Zoran Arsov  Biotechnology  Researcher  2004 - 2008  134 
3.  04584  PhD Franci Demšar  Administrative and organisational sciences  Researcher  2004  252 
4.  24407  PhD Iztok Dogša  Biotechnology  Junior researcher  2005 - 2007  188 
5.  15291  PhD Andrej Duh  Computer science and informatics  Researcher  2004 - 2008  51 
6.  06778  PhD Orest Jarh  Physics  Researcher  2004 - 2008  131 
7.  21546  PhD Tilen Koklič  Physics  Researcher  2004 - 2008  134 
8.  30633  Sandra Kure    Technical associate  2008  16 
9.  24013  PhD Samo Lasič  Physics  Researcher  2005 - 2008  32 
10.  07094  Bojan Ložar  Physics  Technical associate  2004 - 2008  20 
11.  14574  PhD Mojca Urška Mikac  Physics  Researcher  2004 - 2008  148 
12.  16355  PhD Aleš Mohorič  Physics  Researcher  2004 - 2008  405 
13.  08742  Marjanca Nemec    Technical associate  2004 - 2008  81 
14.  03070  PhD Slavko Pečar  Pharmacy  Researcher  2004 - 2008  415 
15.  07777  PhD Gorazd Planinšič  Physics  Researcher  2004 - 2008  529 
16.  00393  PhD Milan Valter Schara  Physics  Researcher  2004 - 2008  343 
17.  07925  Ana Sepe    Technical associate  2004 - 2008  131 
18.  12056  PhD Igor Serša  Physics  Researcher  2004 - 2008  464 
19.  02018  PhD Janez Stepišnik  Physics  Researcher  2004 - 2008  311 
20.  01119  PhD Marjeta Šentjurc  Biochemistry and molecular biology  Researcher  2004 - 2008  511 
21.  18273  PhD Janez Štrancar  Physics  Head  2004 - 2008  361 
Organisations (2)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0106  Jožef Stefan Institute  Ljubljana  5051606000  88,610 
2.  1554  University of Ljubljana, Faculty of Mathematics and Physics  Ljubljana  1627007  33,891 
Based on numerous experiences in various experimental techniques and approaches of electron paramagnetic resonance spectroscopy-EPR (like spin labelling-SL EPR, concentration imaging-CI EPR, kinetic imaging-cI EPR and one-dimensional imaging-1D EPR) as well as expert knowledge in development of the tools for simulation of complex biosystem, characterization like biomembranes and membrane proteins we will continue the research on: -glycosylated cell surfaces, their rheology, dynamics and function based on spin labelling of the cell surfaces, simulation of the aggregation of sugar oligomers and SAXS measurements (small angle X-ray scattering), -the signal transduction pathways and different interaction schemes between the constituents of biomembranes like enzymes, pumps, receptors, membrane domains and rafts, glycocalyx, etc.; based on those findings the possibilities to apply of lipid model systems in the development of lipid-based biosensors will be explored, -the functional properties of particular membrane proteins with site-directed spin labelling and exploration of their conformational freedom as well as low-resolution structure based on SDSL EPR and GHOST condensation results, -the effects of bioactive substances (chemotherapeutics, toxins, anaesthetics, etc.) on the lateral structure and function of membrane domains and the antioxydative properties of model cells and cells from different cell lines, with special focus on nonlinear phenomena in biosystems -the structure of the solid lipid nanoparticles for targeted drug delivery to tissues with special emphasis on understanding of the mechanisms of transport, partitioning and interaction of the nanostructures with cells (fusion, endocythosis, adsorption) -the reactive free radicals and protection against them with methods based on spin traps -the effect of oxygenation of cells and tissues in various pathological processes in vivo as well as the effect of various therapies (radiotherapy, chemotherapy, electrotherapy and their combinations) will be explored with the method of EPR oxymetry In the second part of our research with magnetic resonance we will explore biological processes in vivo and in vitro. It is the spectroscopy using hydrogen and phosphorous nuclei. -Processes of dissolution of blood cloths,where the dynamical MR imaging was used to describe the efficiency of different drugs and approaches that help to dissolve the blood cloths in an artificial blood circulation system. Such research leads to improvement of healing treatments at conditions of infarction. -The use of MR in dentistry will show that MR microscopy provides more detailed images of the dental pulp, as the presently applied X-ray images. This is especially important and helpful in ortodontic treatments in dentistry. -The growth of tree and the reparation of damage is related with the distribution of water in the damaged tissue. Here MR microscopy provides highly selective images showing the distribution of water in the wood. -Exploration of porous material with MR to describe the diffusion process of molecules. These processes are drastically different as compared with non-hindered liquids, since here the active space available is the system of channels determined by the porous medium. The dynamics of molecular movements must include the collisions with the walls of channels that can be only understood with modern methods to measure the diffusion. MRI belongs to the most promising methods to explore grainy materials, especially to follow the mobility of the grain particles. -MRI is a nondestructive method to take images in a randomly chosen cross-section of the sample and the measurement of the speed of the motion of these particles. Between the important problems where MRI can be efficient: study of the convective flows, imaging of distribution of the mechanical stresses before the onset of gliding of the grain particles.
Significance for science
Numerous publications in scientific journals with high impact factor, as well as numerous invited lectures of the group members at international conferences and universities prove that the investigations performed within this program contribute significantly to the global knowledge. We have developed new method on the molecular level for characterizing proteins and their complexes based on SDSL EPR and simulations of local conformational spaces, which represents an alternative method to well-established high-resolution methods, which exhibit serious limitation for systems at physiological conditions and in fast dynamical modes. By his method we were able to determine the structure of main coat protein of bacteriophage M13 in lipid bilayers as well as C-terminal part of nucleoprotein of measles virus in the complex with XD part of phosphoprotein of the same virus. By the development of new methodology based on EPR spectroscopy, EPR spectra simulation, dHEO optimization and GHOST condensation we have contributed to the understanding of one of the famous problems in the current membrane biophysics i.e the problem of lateral membrane structural organization or membrane domains, their role in intercellular interactions and in interactions with bioactive compounds. In combination with small angle x-ray scattering (SAXS), and attenuated total reflection infrared spectroscopy (ATR-FTIR) we have enabled research on biologically relevant nanosecond time scale at physiological conditions of those complex systems, which are to sensitive to external conditions and cannot be investigated by straightforward methods. Results are changing the old paradigm, which states that biological membranes are inactive matrix in which membrane proteins that carry out all membrane cell processes are located. On the contrary, our research has revealed important role of membrane domains, glycosylated membrane surfaces and different water dynamics on membrane surfaces. Presented activities enable research of interactions of bioactive substances and nanoparticles with biological systems, from which our applicative research of antimicrobial surface has originated. With the development of special methods of MRI, particularly fast imaging method, diffusion imaging and imaging in a weak magnetic field a nondestructive and more efficient insight into unknown dynamical phenomena and structural organization in micrometer region in biological systems in vivo is enabled. With new methods we have contributed to the understanding of mechanism of appearance and disintegration of cellular aggregates like thrombus and disintegration of blood clot. By improvement of contrast of MRI methods controlled release of drugs from the tablets was enabled. A new nondestructive, fast and accurate method for moisture content determination was developed on the basis of its mass and the amplitude of the NMR signal, while high resolution 3D MRI enables to determine the anatomic structure of wood structure and internal water distribution. By the development of imaging methods in weak magnetic field new research dimensions are opened as relaxation dynamic is different from the one in high field enabling complementary measurements of spectra and spin-spin interactions. Possible findings can be very important for understanding of mechanisms of pathological processes and in their therapy. Our research work is interdisciplinary oriented in natural sciences, biotechnology and medicine. Scientific knowledge is spread from physics to biology, pharmacy and medicine, by cooperation of different experts. At the same time the physical approach will enable the discovery of mechanism of structural organization, self assembly as well as dynamics of complex biological systems.
Significance for the country
Structural investigations of protein complexes contribute to the development of new anti-viral drugs, while the investigations of membranes, tissues and organisms lead to better understanding of mechanism of action and interactions in biological systems and to understanding of pathologic conditions like cancer, cardiovascular diseases, etc. With the development of EPR oximetry in vivo, we influence also the development of new anti-cancer drugs and efficacy and safety of drug delivery systems, which is important for pharmaceutical industry. Knowledge about the interactions in biological membranes contributes to the development of biosensors enabling the control of pesticides in food and in the environmental samples as well as detection of neurotoxins. Understanding the cells-nanoparticles interactions leads to interesting and safe applications of self-cleaning surfaces, important also for industry, as already proven by the existing collaborations with our industrial partners (Gorenje, Vinprom) and with Veterinary administration of RS with respect to the development of alternative methods for microbiologically clean surfaces in storage rooms and premises for food production. With the development of MRI we participate directly to the development of new medical diagnostic methods in vivo and to education of persons performing clinical diagnostics. In this way we directly improve the quality of health conditions. Development of MRI is also important for healing of blood clots and lungs emboli and tracking the drug delivery pathways. It also enables optimization of heat treatment of food, for example: control of quality of instant food products, baking etc. Knowledge about translational dynamics leads to the understanding of ways of motion in complex systems and to the improvement of technological processes. All the time the group pays an attention to the transfer of highly educated specialists (young PhDs). E.g. this year one of our PhDs got a position in Lek after finishing her PhD, another one got the position as assistant at Biotechnical faculty, UL. Currently, we supervise 3 young researchers in addition to one young scientist from company Ekoprodukt. With respect to the transfer of knowledge to industry we should stress the installation of ultrasound testing of cement quality (Anhovo, Srpenica). By special attention devoted to the improvement of education and popularization of sciences, being one of important aims of the group, we stimulate abstract thinking of students. Consequently, we establish a uniform picture; from the microscopic picture about composition of matter and dynamics of microscopic particles to their connection with macroscopic properties of materials and living systems. With new approaches in educational process targeted to primary and secondary education levels we stimulate innovative thinking and higher cognitive capabilities, which will influence the education and increase the competitiveness of Slovenian economy on a long term basis.
Most important scientific results Final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Final report, complete report on dLib.si
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