{"id":6236,"date":"2023-08-29T09:05:21","date_gmt":"2023-08-29T09:05:21","guid":{"rendered":"https:\/\/www-f5.ijs.si\/about-the-f5-department\/experimental-biophysics-of-complex-systems\/"},"modified":"2026-10-02T11:26:23","modified_gmt":"2026-10-02T11:26:23","slug":"experimental-biophysics-of-complex-systems","status":"publish","type":"page","link":"https:\/\/www-f5.ijs.si\/en\/about-the-f5-department\/experimental-biophysics-of-complex-systems","title":{"rendered":"Experimental Biophysics of Complex Systems"},"content":{"rendered":"\n<div class=\"wp-block-gutena-tabs gutena-tabs-block gutena-tabs-block-ab1065-b5 mobile-scroll\"><ul class=\"gutena-tabs-tab tab-left\"><li class=\"gutena-tab-title active\" data-tab=\"1\"><div class=\"gutena-tab-title-content icon-top\"><div class=\"gutena-tab-title-text\"><div>About research group<\/div><\/div><\/div><\/li><li class=\"gutena-tab-title inactive\" data-tab=\"2\"><div class=\"gutena-tab-title-content icon-top\"><div class=\"gutena-tab-title-text\"><div>Members<\/div><\/div><\/div><\/li><li class=\"gutena-tab-title inactive\" data-tab=\"3\"><div class=\"gutena-tab-title-content icon-top\"><div class=\"gutena-tab-title-text\"><div>Equipment<\/div><\/div><\/div><\/li><\/ul><div class=\"gutena-tabs-content is-layout-flow wp-block-gutena-tabs-is-layout-flow\">\n<div class=\"wp-block-gutena-tab gutena-tab-block gutena-tab-block-1caff8-49 active\" data-tab=\"1\">\n<p class=\"eplus-wrapper wp-block-paragraph\"><strong>Head: <\/strong> Assisant  Professor Iztok Urban\u010di\u010d <\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><strong>Code:<\/strong>&nbsp;P1-0060<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><strong>Duration:<\/strong>January 1, 2019-December 31, 2027<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">January 1, 2015\u2013December 31, 2018, head: Professor \u0160trancar Janez, PhD<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">January 1, 2009-December 31, 2014, head: Professor Ser\u0161a Igor, PhD<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">January 1, 2004-December 31, 2008, head: Professor \u0160trancar Janez, PhD<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><strong>International collaboration:<\/strong>\u00a0<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Institute of Biophysics and Nanosystems Research (A)<br>Helmholtz Munich (DE)<br>Technische Universit\u00e4t Ilmenau (DE)<br>Friedrich Schiller University Jena, Leibniz Centre for Photonics in Infection Research, and Jena Center<br>for Soft Matter, Jena, Germany (DE)<br>NRCWE \u2013 National Research Centre for the Working Environment (DK)<br>Elettra Sinhrotron Trst (I)<br>University of Florence (I)<br>Kyung Hee Univeristy (KR)<br>Wageningen University (NL)<br>STAMI \u2013 National Institute of Occupational Health (NO)<br>University of Bergen (NO)<br>Yale University, School of Medicine, New Haven, CT (ZDA)<br>Mayo Clinic, Rochester MN (ZDA)<br>The University of Utah, Salt Lake City UT (ZDA)<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><a href=\"https:\/\/lbf.ijs.si\/\" rel=\"noreferrer noopener\" target=\"_blank\">Laboratory of Biophysics<\/a><\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><a href=\"https:\/\/titan.ijs.si\/MRI\/index.html\" rel=\"noreferrer noopener\" target=\"_blank\">MRI Laboratory<\/a><\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><\/p>\n\n\n\n<hr class=\" wp-block-separator has-alpha-channel-opacity eplus-wrapper\"\/>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Our program group investigates the structure of biological systems and their function in health and<br>disease by developing and implementing new advanced experimental techniques based around<br>optical microscopies and magnetic resonance imaging.<br>In the Laboratory of Biophysics , we study the environmental triggering and early development of<br>chronic diseases by observing the interactions between (nano)materials, chemicals, and living cells<br>with advanced optical microscopies, trying to understand how small changes in the functioning of<br>cell structures trigger and influence the development of diseases. In cooperation with our spin-out<br>Infinite Biotech, we integrate this knowledge into digital twins that predict the evolution of several<br>\u201cdiseases of civilization\u201d: cancer, neurodegeneration, and chronic lung inflammation. In doing so, we<br>aim to replace the long and costly animal experiments that are currently used for safety testing of<br>chemicals and materials, with quick and high-throughput live-cell fluorescence microscopy, image<br>analysis, automated extraction of the disease mechanism and computer modeling to predict the<br>material safety and disease development.<br>To open new possibilities for investigations of living biological systems, we are developing and<br>implementing advanced optical microscopies, including spectrally-resolved super-resolution STED<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">and two-photon (2PE) microscopy, multichannel fluorescence lifetime imaging (spFLIM),<br>fluorescence microspectroscopy (FMS), structured illumination microscopy (SIM), 2.5D projection<br>imaging, and label-free optical microscopies. To maximize the efficiency of imaging, we are also<br>developing automated and intelligent autonomous microscopy, and novel fluorescent probes.<br>In the MRI laboratory , we have developed a method of magnetic resonance imaging with coils with a<br>nonlinear magnetic field, which are used for spatial signal encoding instead of the usual gradient<br>coils. The method was first explained theoretically and then experimentally verified.<br>We introduced a computer simulation procedure based on the chemical bond fluctuation method.<br>We have successfully used this approach to explain the dissolution processes of tablets based on a<br>polymer matrix in various media.<br>We have adapted magnetic resonance imaging to monitor the processes of dendrite growth in<br>lithium metal batteries. For this purpose, we have also developed a special form of lithium<br>symmetric cell, which is adapted to magnetic resonance imaging. The growth process was monitored<br>with this type of cell for various battery charging conditions.<br>Diffusion tensor magnetic resonance imaging is one of the most advanced methods of medical<br>imaging diagnostics. We have used this method under magnetic resonance microscopy conditions to<br>study the diffusion properties of peripheral nerves. We have also studied how these properties<br>change in various disease states. This research was conducted in collaboration with the Institute of<br>Anatomy of the Faculty of Medicine of the University of Ljubljana.<\/p>\n\n\n\n<hr class=\" wp-block-separator has-alpha-channel-opacity eplus-wrapper\"\/>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">In the Laboratory of Biophysics we achieved major breakthroughs in understanding the initiation and<br>early progression of environmentally-triggered cancer and neurodegeneration. Together with our<br>spin-out Infinite Biotech, the Yale School of Medicine (USA), and the consortium of the 3 M\u20ac EU<br>project nanoPASS that we are coordinating, we showed how exposure to diesel exhaust can cause<br>more aggressive cancers , and developed a cell model that replicates hallmarks of neurodegeneration<br>after exposure to particulate matter.<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Diesel exhaust can disrupt cell division and lead to binuclear cell formation, which is linked to<br>more aggressive cancers<br>We have shown that combustion products such as diesel exhaust interfere with cell division, which<br>can lead to whole-genome duplication and the formation of cells with two or more nuclei, a specific<br>type of genetic change in cancer cells that can enhance metastasis and lead to more aggressive<br>tumors. This achievement was the result of monitoring the process of cell division in real time for<br>over 50 environmental pollutants using an automated live-cell high-throughput approach developed<br>together with our spin-out Infinite Biotech (Figure 1). Our finding were additionally confirmed by<br>Prof. Sheltzer&#8217;s group from Yale School of Medicine who observed that the mutational signature of<br>stem cells exposed to polycyclic aromatic hydrocarbons (PAHs) found in diesel exhaust was similar to<br>mutations found in aggressive cancers with more frequent whole-genome duplication. Our<br>combined observations were the first observed evidence that environmental pollution drives whole-<br>genome duplication, and were published in Brown, Nature communications, 2024 .<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><\/p>\n\n\n\n<figure class=\" wp-block-image aligncenter size-full eplus-wrapper\"><img loading=\"lazy\" decoding=\"async\" width=\"556\" height=\"280\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_1.png\" alt=\"\" class=\"wp-image-9227\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_1.png 556w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_1-300x151.png 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_1-200x101.png 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_1-400x201.png 400w\" sizes=\"auto, (max-width: 556px) 100vw, 556px\" \/><figcaption class=\"wp-element-caption\">Figure 1: Example of whole genome duplication and binuclear cell formation (pink arrows)<br>induced by particulate matter from polluted air in a cellular model of chronic lung<br>inflammation.<\/figcaption><\/figure>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">New in vitro cell model for better understanding of neurodegeneration and preclinical screening of<br>drug candidates.<br>We have established an environmentally-induced in vitro cell coculture model of local<br>neurodegeneration able to exhibit most of the cellular hallmarks of neurodegeneration when<br>exposed to various environmental particulates and engineered nanoparticles (Figure 2). In contrast,<br>most currently used rodent models genetically recapitulate protein aggregation seen in the patient<br>brains, but do not show neuronal degeneration, imposing challenges for testing of drug candidates.<br>Our model thus offers a promising new platform for mechanistic investigations of causes and<br>mechanistic progression of Alzheimer\u2019s disease, as well as for preclinical screening of drug<br>candidates. The results were published in a prominent journal in the field of nanotoxicology research<br>Nanotoxicology ( Sebastijanovi\u0107, Nanotoxicology, 2024 ).<\/p>\n\n\n\n<figure class=\" wp-block-image size-full eplus-wrapper\"><img loading=\"lazy\" decoding=\"async\" width=\"601\" height=\"348\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_2.png\" alt=\"\" class=\"wp-image-9229\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_2.png 601w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_2-300x174.png 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_2-200x116.png 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_2-400x232.png 400w\" sizes=\"auto, (max-width: 601px) 100vw, 601px\" \/><\/figure>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Figure 2. Pathologies observed in differentiated neurons (green cytosol) exposed to anatase<br>TiO 2 nanotubes (red). Left: extracellular plaques containing amyloid-\u03b2 (blue) and tau protein<br>(gray); Right: rupture of neuronal connections (yellow arrows).<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Development and application of advanced optical microscopy methods: SiM microscopy,<br>intelligent autonomous microscopy, novel fluorescent probes, and spectral STED microscopy<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">For the newly established Center of Advanced Optical Microscopies (CNOM), which operates within<br>the scope of the Center for Electron Microscopy and Microanalysis (CEMM), we successfully<br>continued building the cutting-edge high-throughput fluorescence microscope, which combines<br>Structured Illumination microscopy (SIM) (achieving the expected 1.75 resolution improvement over<br>confocal microscopy) and 2.5D microscopy, and are adding the remaining QPI modality (Figure 3).<br>The system is fully automated with an easy-to-use user interface, enabling multi-day imaging of a<br>multitude of samples, including live cells. Our goal is to complete the system by the end of<br>September 2025 with a hands-on demonstration to the wider community at J. Stefan Institute.<\/p>\n\n\n\n<figure class=\" wp-block-image size-full eplus-wrapper\"><img loading=\"lazy\" decoding=\"async\" width=\"1009\" height=\"566\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3.png\" alt=\"\" class=\"wp-image-9231\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3.png 1009w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3-300x168.png 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3-768x431.png 768w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3-200x112.png 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3-400x224.png 400w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3-600x337.png 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3-800x449.png 800w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_3-1000x561.png 1000w\" sizes=\"auto, (max-width: 1009px) 100vw, 1009px\" \/><\/figure>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Figure 3. Custom fluorescence microscope that combines super-resolution imaging (SIM),<br>projection imaging (2.5D) and label-free microscopy (QPI), built in-house in the Center for<br>Advanced Optical Microscopies.<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">We are using the algorithms developed within the projects on autonomous microscopy (in<br>collaboration with the Faculty of Computer and Information Science, University of Ljubljana) for<br>characterization of sparse nuclear RNA-protein condensates, which appear to be crucial in the<br>regulation of embryonic development (collaboration with the group of dr. Miha Modic\/prof. Jernej<br>Ule, National Institute of Chemistry, Ljubljana, and Francis Crick Institute, London, UK).<br>We tested and characterized several novel fluorescent probes and intracellular sensors for advanced<br>microscopy and microspectroscopy techniques, which were synthesized at the Faculty of Pharmacy<br>(University of Ljubljana) ( Kokot, Bioorganic chemistry, 2024 ).<br>With collaborators from University of Oxford (prof. C. Eggeling, now at University of Jena, Germany),<br>we characterized the unexpected phenomenon of photoblueing, i.e. the process where the<br>spectrum of a fluorescent dye shifts towards lower wavelengths after being exposed to high laser<br>powers, used in fluorescence microscopy ( Dasgupta, Nature methods, 2024 ). The detailed<br>characterization of this phenomenon was enabled by our unique combination of a STED microscope<br>equipped with a spectral detector.<\/p>\n\n\n\n<hr class=\" wp-block-separator has-alpha-channel-opacity eplus-wrapper\"\/>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Dissolution simulation of polymer matrix tablets<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Polymer matrix tablets are an important oral drug delivery system today. In this study, magnetic<br>resonance microscopy (MRM) was used to analyze the water hydration process in xanthan-based<br>tablets by measuring erosion, swelling, and penetration fronts. These experimental results were<br>then complemented by numerical simulations of the same process, i.e. the polymer matrix of the<br>tablet is modeled as an assembly of interacting chains with embedded drug particles, while its<br>hydration process is mediated by interactions with solvent particles (Figure 4). The swelling<br>dynamics were modeled using a Monte Carlo-based bond-fluctuation model (BFM), which elegantly<br>accounts for steric and nearest-neighbor interactions. The study, published in: (Bajd, Polymers,<br>2024), provides an efficient experimental-theoretical approach to studying polymer matrix swelling<br>processes.<\/p>\n\n\n\n<figure class=\" wp-block-image size-large eplus-wrapper\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"975\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-1024x975.jpg\" alt=\"\" class=\"wp-image-9233\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-1024x975.jpg 1024w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-300x286.jpg 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-768x731.jpg 768w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-200x190.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-400x381.jpg 400w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-600x571.jpg 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-800x762.jpg 800w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-1000x952.jpg 1000w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4-1200x1143.jpg 1200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_4.jpg 1346w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Fig. 4: A flowchart schematically summarizing the essential steps in (a) magnetic resonance imaging<br>(MRI) experiments of polymer tablet swelling enabling the determination of erosion, swelling and<br>penetration fronts (EF, SF, PF) and in (b) explicit-solvent 2D bond fluctuation model (BFM)<br>simulations of the swelling process of drug-containing polymer matrices.<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Magnetic resonance imaging and simulation of dendritic growth in lithium metal batteries<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">We developed a new simulation model of dendrite growth based on the diffusion-limited<br>aggregation (DLA) algorithm upgraded with consideration of the electric field, which improved the<br>model&#8217;s ability to simulate realistic dendrite morphologies. The model predictions were also<br>confirmed by experimental data on dendrite structures measured by sequential 3D MRI (Figure 5).<br>This approach provides researchers with a practical tool to explore different strategies for inhibiting<br>dendrite growth, ultimately contributing to the development of safer and more reliable lithium-ion<br>batteries. The research was published in: (Peklar, Batteries, 2024).<\/p>\n\n\n\n<figure class=\" wp-block-image size-large eplus-wrapper\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"629\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-1024x629.jpg\" alt=\"\" class=\"wp-image-9235\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-1024x629.jpg 1024w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-300x184.jpg 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-768x472.jpg 768w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-200x123.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-400x246.jpg 400w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-600x369.jpg 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-800x492.jpg 800w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-1000x615.jpg 1000w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5-1200x738.jpg 1200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2026\/10\/Figure_5.jpg 1360w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Fig. 5: MRI imaging results; a representative slice showing the development of the dendritic<br>structure with time (a). A time sequence of volume-rendered images of dendrite binary masks<br>extracted from the corresponding MR images of the battery (b).<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Magnetic resonance imaging using nonlinear magnetic field coils for spatial signal encoding<br>Previous approaches to MR imaging using nonlinear magnetic field coils for spatial signal encoding<br>share a complex reconstruction procedure that originates from the interpretation of the signal in the<br>spatial frequency domain (k-space), which in our opinion is somewhat misleading and suboptimal.<br>Instead, we propose a reconstruction approach in which the acquired MR signal is generalized and<br>thus treated as a function of time rather than as a function of k-space. This time-domain signal is<br>then Fourier transformed into a spectrum, which usually represents a distorted image of the sample.<br>In a second step, this spectrum is geometrically and intensity corrected according to the known<br>frequency-to-space (magnetic field-to-space) transformation of the encoding coil. The use of such<br>coils in MR imaging could have a significant impact on the imaging speed due to the possible design<br>of such coils with low inductance. In the article (Tu\u0161ar, Scientific Reports, 2024), we also<br>experimentally verified the presented theory.<br>Assessment of dental pulp changes in caries based on MR imaging and histology<br>In this study, we assessed the correlation between NMR T 2 relaxation times and their variability with<br>histopathological results of the same patient&#8217;s teeth in relation to caries progression. The study<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">included 52 extracted permanent premolars whose T 2 times were measured byT 2 mapping before<br>extraction, and caries progression was assessed using the ICDAS scale. We found a positive<br>correlation between T 2 times and pulp vessel density and a negative correlation between T 2 times and<br>macrophage density. The results of the study, which was published in: (Tenyi, BMC Oral Health,<br>2024), confirmed the usefulness of MRI in assessing the actual condition of pulp tissue.<br>Development of a driven equilibrium spin echo MR imaging sequence<br>In this study, we aimed to find an efficient solution for fast MR imaging of samples with long NMR<br>relaxation times T 1 . Namely, most imaging sequences for this purpose have distortions originating<br>from non-uniform k-space weighting or T 2 * signal weighting. To avoid these problems, we developed<br>a double spin echo imaging sequence, which achieves almost complete preservation of the<br>longitudinal magnetization after each signal acquisition, in contrast to the standard spin echo<br>sequence, where it is zero. This allows us to perform very fast imaging of the aforementioned<br>samples with low image distortions. This method, published in: (Ser\u0161a, J. Magn. Reson., 2024), was<br>theoretically analyzed and verified under the conditions of microscopic MR imaging.<br>Diffusion tensor imaging of peripheral nerves with magnetic resonance microscopy<br>We compared three-dimensional (3D) reconstructions of the median and ulnar nerves obtained by<br>high-resolution tomographic ultrasound (HRUS) and magnetic resonance microscopy (MRM), and<br>assessed the ability of both methods to visualize intraneural anatomy. We found that 3D HRUS<br>underestimates nerve and fascicle volume compared to MRM, and also shows fewer fascicles and<br>approximately half fewer interfascicular connections. The study was published in: (Pu\u0161nik, Eur.<br>Radiol. Exp., 2024).<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Training of young experts<br>In 2024, 2 PhD candidates (Sebastijanovi\u0107, Dodlek) and 18 MSc students defended their theses.<\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Selected publications in 2024<\/p>\n\n\n<ol class=\" wp-block-list eplus-wrapper eplus-styles-uid-d5fcdf\">\n<li class=\" eplus-wrapper\">Peklar, Rok, Mikac, Ur\u0161ka, Ser\u0161a, Igor. Simulation of dendrite growth with a diffusion-limited<br>aggregation model validated by MRI of a lithium symmetric cell during charging. Batteries.<br>2024, vol. 10, iss. 10, str. 1-15, ilustr. ISSN 2313-0105. <a href=\"https:\/\/www.mdpi.com\/2313-\">https:\/\/www.mdpi.com\/2313-<\/a><br>0105\/10\/10\/352 , DOI: 10.3390\/batteries10100352 . [COBISS.SI-ID 210864643 ]<\/li>\n\n\n\n<li class=\" eplus-wrapper\">Tu[ar, Kaja, Ser\u0161a, Igor. Use of nonlinear pulsed magnetic fields for spatial encoding in<br>magnetic resonance imaging. Scientific reports. 2024, vol. 14, art. 7521, 15 str. ISSN 2045-<\/li>\n\n\n\n<li class=\" eplus-wrapper\">DOI: 10.1038\/s41598-024-58229-x . [COBISS.SI-ID 191262723 ],<\/li>\n\n\n\n<li class=\" eplus-wrapper\">Bajd, Franci, Mikac, Ur\u0161ka, Mohori\u010d, Ale\u0161, Ser\u0161a, Igor. The effect of polymer\u2013solvent<br>interaction on the swelling of polymer matrix tablets: a magnetic resonance microscopy<br>study complemented by bond fluctuation model simulations. Polymers. Mar. 2024, vol. 16,<br>iss. 5, [article no.] 601, str. 1-14, ilustr. ISSN 2073-4360. <a href=\"https:\/\/www.mdpi.com\/2073-\">https:\/\/www.mdpi.com\/2073-<\/a><br>4360\/16\/5\/601 , Repozitorij Univerze v Ljubljani \u2013 RUL , DOI: 10.3390\/polym16050601 .<br>[COBISS.SI-ID 186456835 ]<\/li>\n\n\n\n<li class=\" eplus-wrapper\">Brown, L. M. et al. An elevated rate of whole-genome duplications in cancers from Black<br>patients. Nat Commun 15, 8218 (2024).<\/li>\n\n\n\n<li class=\" eplus-wrapper\">Sebastijanovi\u0107, A. et al. Particulate matter constituents trigger the formation of extracellular<br>amyloid \u03b2 and Tau -containing plaques and neurite shortening in vitro. Nanotoxicology 18,<br>335\u2013353 (2024).<\/li>\n\n\n\n<li class=\" eplus-wrapper\">Dasgupta, A. et al. Effects and avoidance of photoconversion-induced artifacts in confocal<br>and STED microscopy. Nature Methods 21, 1171-1174 (2024).<\/li>\n<\/ol><\/div>\n\n\n\n<div class=\"wp-block-gutena-tab gutena-tab-block gutena-tab-block-6cf5d7-e0 inactive\" data-tab=\"2\">\n<figure class=\"eplus-wrapper is-style-stripes wp-block-table\"><table class=\"has-fixed-layout\"><thead><tr><th><strong>Name and Surname<\/strong><\/th><th><strong>Role<\/strong><\/th><th><strong>Laboratory<\/strong><\/th><th><strong>Room number<\/strong><\/th><\/tr><\/thead><tbody><tr><td>Janez \u0160trancar<\/td><td>Head of the research group<\/td><td>LBF<\/td><td>J109<\/td><\/tr><tr><td>Franci Bajd<\/td><td>Researcher<\/td><td>MRI<\/td><td>&nbsp;<\/td><\/tr><tr><td>Eva Cerkvenik<\/td><td>Technician<\/td><td>LBF <\/td><td>\u00a0J111<\/td><\/tr><tr><td>Tilen Kokli\u010d <\/td><td>Researcher<\/td><td>LBF<\/td><td>\u00a0J110<\/td><\/tr><tr><td>Bo\u0161tjan Kokot <\/td><td>Researcher<\/td><td> LBF <\/td><td>\u00a0J108<\/td><\/tr><tr><td>Hana Kokot <\/td><td>Researcher <\/td><td>LBF<\/td><td> \u00a0J108<\/td><\/tr><tr><td>Mojca Ur\u0161ka Mikac <\/td><td>Researcher <\/td><td>\u00a0MRI<\/td><td>\u00a0J418A, 009A<\/td><\/tr><tr><td>Ale\u0161 Mohori\u010d <\/td><td>Researcher<\/td><td>MRI<\/td><td>&nbsp;<\/td><\/tr><tr><td>Rok Peklar <\/td><td>Young Researcher<\/td><td>MRI<\/td><td><\/td><\/tr><tr><td>Ana Sepe <\/td><td>Technician <\/td><td>MRI<\/td><td>009A, C304<\/td><\/tr><tr><td>Igor Ser\u0161a <\/td><td>Head of laboratory<\/td><td>MRI <\/td><td>\u00a0J418A, 009A<\/td><\/tr><tr><td>Cody Tripp <\/td><td>Technician <\/td><td>LBF<\/td><td>J111<\/td><\/tr><tr><td>Iztok Urban\u010di\u010d <\/td><td>Researcher<\/td><td>LBF <\/td><td> J107<\/td><\/tr><\/tbody><tfoot><tr><td><\/td><td><\/td><td><\/td><td><\/td><\/tr><\/tfoot><\/table><\/figure>\n<\/div>\n\n\n\n<div class=\"wp-block-gutena-tab gutena-tab-block gutena-tab-block-c28bed-db inactive\" data-tab=\"3\">\n<h2 class=\"eplus-wrapper wp-block-heading\"><strong>Laboratory for cultivation of bacteria<\/strong><\/h2>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Equipment: C2 laminar flow cabinet, incubator, shaker, fume hood, spectrophotometer, centrifuge, Nikon fluorescent microscope with cell-counting software, different lenses and computer-controlled stage<\/p>\n\n\n\n<div class=\"column-3 eplus-wrapper wp-block-group is-layout-flow wp-block-group-is-layout-flow\">\n<figure class=\"eplus-wrapper wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"600\" height=\"432\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32610_1431610769_105_32610.jpg\" alt=\"\" class=\"wp-image-3733\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32610_1431610769_105_32610.jpg 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32610_1431610769_105_32610-300x216.jpg 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32610_1431610769_105_32610-200x144.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32610_1431610769_105_32610-400x288.jpg 400w\" sizes=\"auto, (max-width: 600px) 100vw, 600px\" \/><\/figure>\n\n\n\n<figure class=\"eplus-wrapper wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"600\" height=\"452\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32632_1431610769_230_32632.jpg\" alt=\"\" class=\"wp-image-3732\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32632_1431610769_230_32632.jpg 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32632_1431610769_230_32632-300x226.jpg 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32632_1431610769_230_32632-200x151.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32632_1431610769_230_32632-400x301.jpg 400w\" sizes=\"auto, (max-width: 600px) 100vw, 600px\" \/><\/figure>\n\n\n\n<figure class=\"eplus-wrapper wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"600\" height=\"454\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32661_1431610770_28_32661.jpg\" alt=\"\" class=\"wp-image-3731\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32661_1431610770_28_32661.jpg 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32661_1431610770_28_32661-300x227.jpg 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32661_1431610770_28_32661-200x151.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/32661_1431610770_28_32661-400x303.jpg 400w\" sizes=\"auto, (max-width: 600px) 100vw, 600px\" \/><\/figure>\n<\/div>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><strong>Laboratory for cultivation of eukaryotic cells<\/strong><\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Equipment: laminar flow cabinet, incubator, ultracentrifuge, -70\u00b0C refrigerator, other minor equipment<\/p>\n\n\n\n<div class=\"column-3 eplus-wrapper wp-block-group is-layout-flow wp-block-group-is-layout-flow\">\n<figure class=\"eplus-wrapper wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"600\" height=\"451\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/567_1431610976_410_567.jpg\" alt=\"\" class=\"wp-image-3737\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/567_1431610976_410_567.jpg 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/567_1431610976_410_567-300x226.jpg 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/567_1431610976_410_567-200x150.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/567_1431610976_410_567-400x301.jpg 400w\" sizes=\"auto, (max-width: 600px) 100vw, 600px\" \/><\/figure>\n\n\n\n<figure class=\"eplus-wrapper wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"430\" height=\"600\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/585_1431610976_324_585.jpg\" alt=\"\" class=\"wp-image-3736\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/585_1431610976_324_585.jpg 430w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/585_1431610976_324_585-215x300.jpg 215w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/585_1431610976_324_585-200x279.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/585_1431610976_324_585-400x558.jpg 400w\" sizes=\"auto, (max-width: 430px) 100vw, 430px\" \/><\/figure>\n\n\n\n<figure class=\"eplus-wrapper wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"600\" height=\"344\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/612_1431610977_447_612.jpg\" alt=\"\" class=\"wp-image-3735\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/612_1431610977_447_612.jpg 600w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/612_1431610977_447_612-300x172.jpg 300w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/612_1431610977_447_612-200x115.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/612_1431610977_447_612-400x229.jpg 400w\" sizes=\"auto, (max-width: 600px) 100vw, 600px\" \/><\/figure>\n<\/div>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><strong>Buchi R-200 rotary evaporator<\/strong><\/p>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\">Rotary evaporator for preparation of spin films and suspension membranes (liposomes) powered by a water pump with automatic control and pressure regulation<\/p>\n\n\n\n<figure class=\"eplus-wrapper wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"414\" height=\"599\" src=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/794_1431611116_356_794.jpg\" alt=\"\" class=\"wp-image-3734\" srcset=\"https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/794_1431611116_356_794.jpg 414w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/794_1431611116_356_794-207x300.jpg 207w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/794_1431611116_356_794-200x289.jpg 200w, https:\/\/www-f5.ijs.si\/wp-content\/uploads\/2023\/08\/794_1431611116_356_794-400x579.jpg 400w\" sizes=\"auto, (max-width: 414px) 100vw, 414px\" \/><\/figure>\n\n\n\n<p class=\"eplus-wrapper wp-block-paragraph\"><strong>Philips 301 transmission electron microscope (worn-out)<\/strong><\/p>\n\n\n\n<h3 class=\" wp-block-heading eplus-wrapper\"><strong>Perkin-Elmer Lambda 17 UV-VIS spectrophotometer<\/strong><\/h3>\n\n\n\n<h3 class=\"eplus-wrapper wp-block-heading\"><a href=\"https:\/\/www-f5.ijs.si\/en\/dvofotonski-3d-sted-superlocljivi-mikroskop\" target=\"_blank\" aria-label=\"Two-photon 3D STED super-resolution microscope (opens in a new tab)\" rel=\"noreferrer noopener\" class=\"ek-link\">Two-photon 3D STED super-resolution microscope<\/a><\/h3>\n<\/div>\n<\/div><\/div>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"is-style-default eplus-wrapper wp-block-spacer\"><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":6042,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_editorskit_title_hidden":false,"_editorskit_reading_time":0,"_editorskit_is_block_options_detached":false,"_editorskit_block_options_position":"{}","editor_plus_copied_stylings":"{}","footnotes":""},"class_list":["post-6236","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Experimental Biophysics of Complex Systems - In\u0161titut Jo\u017eef Stefan<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www-f5.ijs.si\/en\/about-the-f5-department\/experimental-biophysics-of-complex-systems\" 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