Projects / Programmes source: ARRS

Experimental biophysics of complex systems and imaging in biomedicine

Research activity

Code Science Field Subfield
1.02.00  Natural sciences and mathematics  Physics   

Code Science Field
B002  Biomedical sciences  Biophysics 

Code Science Field
1.03  Natural Sciences  Physical sciences 
Interactions, medical imaging, membranes, supramolecular structures, cells, tissues, nanomaterials, medical devices, light, spectroscopies, microscopies, microspectroscopies, magnetic resonance, MRI, modeling, multimodal imaging, knowledge transfer to technologies, therapies and didactics
Evaluation (rules)
source: COBISS
Researchers (22)
no. Code Name and surname Research area Role Period No. of publications
1.  20208  PhD Zoran Arsov  Biotechnology  Researcher  2015 - 2018  133 
2.  30867  PhD Franci Bajd  Physics  Researcher  2015 - 2018  87 
3.  33037  PhD Sergej Faletič  Physics  Researcher  2015 - 2018  80 
4.  21546  PhD Tilen Koklič  Physics  Researcher  2015 - 2018  132 
5.  38854  Boštjan Kokot  Physics  Technician  2016 - 2018  25 
6.  38855  PhD Hana Kokot  Physics  Junior researcher  2016 - 2018  36 
7.  14574  PhD Mojca Urška Mikac  Physics  Researcher  2015 - 2018  147 
8.  16355  PhD Aleš Mohorič  Physics  Researcher  2015 - 2018  392 
9.  28861  PhD Stane Pajk  Pharmacy  Researcher  2015 - 2018  169 
10.  07777  PhD Gorazd Planinšič  Physics  Researcher  2015 - 2018  520 
11.  34747  PhD Rok Podlipec  Physics  Researcher  2015 - 2018  73 
12.  52062  Aleksandar Sebastijanović  Physics  Junior researcher  2018  12 
13.  07925  Ana Sepe    Technician  2015 - 2018  131 
14.  12056  PhD Igor Serša  Physics  Researcher  2015 - 2018  457 
15.  02018  PhD Janez Stepišnik  Physics  Researcher  2015 - 2018  309 
16.  01119  PhD Marjeta Šentjurc  Biochemistry and molecular biology  Researcher  2015 - 2018  512 
17.  38193  Jan Šömen  Physics  Junior researcher  2015 - 2016 
18.  18273  PhD Janez Štrancar  Physics  Principal Researcher  2015 - 2018  359 
19.  32057  PhD Iztok Urbančič  Physics  Researcher  2015 - 2018  115 
20.  28490  PhD Jernej Vidmar  Cardiovascular system  Researcher  2015 - 2018  84 
21.  51652  Patrycja B. Zawilska  Physics  Technician  2018 
22.  30871  PhD Maja Zorc  Physics  Technician  2015 - 2018  57 
Organisations (2)
no. Code Research organisation City Registration number No. of publications
1.  0106  Jožef Stefan Institute  Ljubljana  5051606000  85,605 
2.  1554  University of Ljubljana, Faculty of Mathematics and Physics  Ljubljana  1627007  31,628 
Recent technological advances aim at improving our health through powerful diagnostics-driven treatments, but at the same time expose us to new materials, devices and technologies that can in principle harm our health. Our program implement methods of biophysics and medical physics to clarify these conflicting effects by unraveling the molecular interactions at the biointerfaces and translating the corresponding mechanisms onto the tissue/organ level by advanced imaging methods. Specifically, the research work will focus on biosystem-nanoparticle interaction, biosystem-polymer interaction, biosystem-light interaction, supramolecular assembly and multimodal imaging. The research strategies will be implemented in new didactical approaches to help students developing strategies in solving experimental problems on the microscopic scale. The research work will be carried in 5 research working packages in addition to 1 research-didactical package in 3 laboratories with complementary state of the art research methods and expertise for spectroscopic, microscopic, microspectroscopic, and imaging techniques as well as pulse sequence designing, modelling and probe synthesis for biophysical and biomedical applications. Many activities will run in cooperation with several international research groups. The research results will boost the understanding of the nanoparticles pathway in organisms, tissues and cells contributing to safer production, application and handling. At the same time the results will improve medical imaging with nanoparticles as effective contrast agents. Nanomaterials will also play a role as bioactive material for antimicrobial protection against infrastructure-resistant bacteria. Unraveling physical mechanisms related to biocompatibility will rationalize new boost in development of medical devices, significantly reducing the costs of such regeneration medicine approaches. Various therapeutic procedures will be impacted by the study of the molecular mechanisms and advances in imaging procedure, especially thrombolytic treatment, cancer treatment by electroporation, hyperthermia and various applications in stomatology. Development in multimodal imaging, i.e. endoscopic imaging that relies on the coupling between endoscopy and microspectroscopic concepts, will directly improve in-real-time diagnostics and accuracy during endoscopic-guided surgery. Guiding the light through membrane stacks and exploring its application can on the other hand bring completely new perspective on neural network function, possibly adding new transduction concept to the well-established membrane-potential dogma. Finally, the strategies of solving the microscopic picture will be directly used to improve student reasoning, run training-by-research of highly motivated students and transferring knowledge into new technologies through new and established cooperation with industrial partners like Krka, Lek, Educell, Optotek and others.
Significance for science
The results of our research program on the scientific frontiers (denoted with black bold text) are expected to provide the scientific breakthroughs (denoted with green bold text) as follows: The era of new materials imposes new forefronts to the biophysics such as unraveling nanomaterials’ transport and accumulation in the organism. On the contrary to the generally accepted understanding that their uptake in tissues and cells is driven by well-controlled specific recognition events, some of the latest studies, including our preliminary results, indicate that unspecific membrane transition can be important as well. Exploration and confirmation of unspecific uptake through real membranes via our recently developed microspectroscopies can result in new understanding of the nanomaterial-cell interactions and the mechanisms of nanosafety in general. Many new materials are intentionally brought in contact with our body for the purpose of regenerative medicine. The inability of predicting their harmful effects exposes the problem of poor understanding of the concept of biocompatibility. We will apply our expert knowledge in structural/motional characterization on molecular scale to clarify the biocompatibility puzzle. In addition, investigation of translational dynamics and diffusion-related processes can characterize properties of the interfaces, impacting the applicability of polymer-based devices including advanced drug-delivery/carrier systems. Significance of light guiding in biosystems has been widely overlooked despite fascinating discoveries in the past. Membrane potential variation and electrochemical signal transduction are so well-established concepts that the unexplained problems look marginal. One of them is synchronization problem in the neural networks, where the speed of signal transduction and the size of the network strangely mismatch the response time of the tissue. Recent findings in optics and optogenetics will initiate new experiments to unravel new light-based signal transduction mechanisms possibly representing major breakthrough in biophysics and neurosciences. Current medical treatment procedures rely on biochemical diagnostics, requiring acquisition of tissue samples and limiting the treatment efficiency monitoring in real time. Therefore strong effort has been put in development of new approaches in medical imaging including image analysis to acquire cellular information at the tissue/organ level in vivo during treatment procedures. Novel MRI methods will therefore provide better differentiation of pathological and healthy tissues, efficient monitoring of magnetic nanoparticles in therapeutic procedures like hyperthermia, new applications in stomatology and improved electroporation therapy by current density distribution imaging. They will also explain the mechanism of formation and disintegration of cellular aggregates like blood clot leading to more efficient thrombolytic agents with less side effects. In addition, our research program impact is expected also in protein (complexes’) structure determination and methodological advances in various hybrid experimental techniques.
Significance for the country
Understanding the interaction between materials, light and devices on one side and biological systems like molecular structures, cells, tissues and organisms on the other side brings new opportunities affecting our health and health-related infrastructure. Some of the materials are intentionally developed for tissue regeneration where understanding of the biocompatibility is foreseen to rationalize and reduce the costs of the development of such medical devices. New ideas like printing, photomasking and layer-by-layer in situ/in vivo protocols, which will be developed, can provide solutions for the currently unsolvable tissue damages like large cartilage defects. On the other hand, new knowledge evolved from studying the interaction between nanomaterials and biological systems can result in new nanomaterial-safety regulations reducing the nano-related health risk, increasing the awareness of safe handling protocols and thus representing the nanomaterial in a more “manageable” perspective. At the same time, nanomaterials’ bactericidal effect can provide antimicrobial infrastructure protection in hospitals and food processing industry, where one can efficiently fight against infrastructure-related and even resistant bacteria like MRSA and Listeria with significant economic burden. Moreover, nanomaterials offer better contrasted biomedical imaging as well resulting in improved therapies and less side-effects. Similar effect will be achieved with development of new imaging techniques and their variants. For example, new advances in MRI imaging enable control of electric field in electroporation increasing the cancer treatment efficiency and reducing the doses of antitumor drugs. In addition, they allow prediction of blood clot dissolution making thrombolytic treatment more efficient. At the same time understanding the molecular mechanisms of blood clot formation can serve in more efficient development of anticoagulation drugs. Finally, the technical advances in microspectroscopies can provide new platform for endoscopic molecular (multimodal) imaging for image-guided surgery. It is important to note that not only the knowledge about (supra)molecular interactions and assembly matters, but also the process of gaining this knowledge by itself. The strategies of solving the microscopic picture will be directly used for didactical purposes to improve student reasoning. In this respect, training-by-research and transfer of the knowledge to young highly motivated people represent the most efficient starting point for future knowledge-driven technology transfers. This will clearly contribute to better education / training process at all university levels and development of biophysics in national framework. In addition, direct knowledge and technology transfer will also be involved in our activities through new and established cooperation with industrial partners like Krka, Lek, Educell, Optotek and others in the fields of delayed-release tablets’ optimization, in-line dispersion quality control, cartilage/meniscus/ligament scaffold development, ophthalmological laser damage control in real time, etc. All these activities will lead to significant progress of the technological level through development of a new product like biomaterial-based biocompatible scaffolds and different pharmaceutical formulations, as well as through development of a new technologies for industrial product and service quality control.
Most important scientific results Annual report 2015, 2016, 2017, final report
Most important socioeconomically and culturally relevant results Annual report 2015, 2016, 2017, final report
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