Projects / Programmes source: ARIS

Biophysics of polymers, membranes, gels, colloids and cells

Research activity

Code Science Field Subfield
1.02.00  Natural sciences and mathematics  Physics   
3.03.00  Medical sciences  Neurobiology   

Code Science Field
1.03  Natural Sciences  Physical sciences 
3.01  Medical and Health Sciences  Basic medicine 
intermolecular interactions, proteins, viral capsids, RNA, colloids, nanoparticles, liquid crystals, graphene, organic-inorganic heterostructures, wetting, hydration, microfluidics, laser tweezers, membranes, vesicles, cells, cell metabolism, signaling, enzymes, tissues, morphogenesis, cancer
Evaluation (rules)
source: COBISS
Data for the last 5 years (citations for the last 10 years) on September 26, 2023; A3 for period 2017-2021
Data for ARIS tenders ( 04.04.2019 – Programme tender , archive )
Database Linked records Citations Pure citations Average pure citations
WoS  1,256  33,312  28,257  22.5 
Scopus  1,222  34,011  29,150  23.85 
Researchers (49)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  56557  Urška Andrenšek  Natural sciences and mathematics  Junior researcher  2022 - 2023 
2.  33760  PhD Lamprini Athanasopoulou  Natural sciences and mathematics  Researcher  2022 - 2023 
3.  11088  PhD Bojan Božič  Medical sciences  Researcher  2022 - 2023  119 
4.  06617  PhD Gvido Bratina  Natural sciences and mathematics  Researcher  2022 - 2023  212 
5.  05483  PhD Milan Brumen  Natural sciences and mathematics  Retired researcher  2022 - 2023  441 
6.  55762  Veronika Bukina  Natural sciences and mathematics  Junior researcher  2022 - 2023 
7.  33752  PhD Manisha Chhikara  Natural sciences and mathematics  Researcher  2022 - 2023  16 
8.  26235  Alenka Cimprič    Technical associate  2022 - 2023 
9.  05974  PhD Mojca Čepič  Social sciences  Researcher  2022 - 2023  815 
10.  18326  PhD Jure Derganc  Medical sciences  Researcher  2022 - 2023  112 
11.  26447  PhD Andrej Dobovišek  Natural sciences and mathematics  Researcher  2022 - 2023  108 
12.  30982  PhD Saša Dolenc (Ziherl)  Natural sciences and mathematics  Researcher  2022 - 2023  99 
13.  57042  Lija Fajdiga  Natural sciences and mathematics  Junior researcher  2022 - 2023 
14.  19553  PhD Aleš Fajmut  Natural sciences and mathematics  Researcher  2022 - 2023  224 
15.  18038  PhD Gregor Gomišček  Natural sciences and mathematics  Researcher  2022 - 2023  91 
16.  26456  PhD Matej Kanduč  Natural sciences and mathematics  Researcher  2022 - 2023  179 
17.  36332  PhD Matej Krajnc  Natural sciences and mathematics  Researcher  2022 - 2023  46 
18.  12001  PhD Janja Majhenc  Natural sciences and mathematics  Researcher  2022 - 2023  73 
19.  23455  PhD Mojca Mally  Medical sciences  Researcher  2022 - 2023  22 
20.  13159  PhD Marko Marhl  Natural sciences and mathematics  Researcher  2022 - 2023  648 
21.  34480  PhD Rene Markovič  Natural sciences and mathematics  Researcher  2022 - 2023  102 
22.  56008  Milan Obradović    Technical associate  2022 - 2023 
23.  54880  PhD Nadiia Pastukhova  Natural sciences and mathematics  Researcher  2022 - 2023  18 
24.  22305  PhD Egon Pavlica  Natural sciences and mathematics  Researcher  2022 - 2023  97 
25.  19225  PhD Mojca Pavlin  Engineering sciences and technologies  Researcher  2022 - 2023  253 
26.  08589  PhD Rudolf Podgornik  Natural sciences and mathematics  Retired researcher  2022 - 2023  702 
27.  36390  Maja Poklinek Čančula  Social sciences  Junior researcher  2022 - 2023 
28.  57499  Lakshmi Rajan  Natural sciences and mathematics  Junior researcher  2023 
29.  32154  PhD Anže Rapoš Božič  Natural sciences and mathematics  Researcher  2022 - 2023  59 
30.  50626  PhD Jernej Repas  Biotechnical sciences  Researcher  2022 - 2023  23 
31.  52061  PhD Jan Rozman  Natural sciences and mathematics  Junior researcher  2022  10 
32.  57355  PhD Tanmoy Sarkar  Natural sciences and mathematics  Researcher  2023 
33.  55840  Tadeja Snedec  Medical sciences  Junior researcher  2022 - 2023 
34.  53852  PhD Fabio Staniscia  Natural sciences and mathematics  Researcher  2022 - 2023  22 
35.  02013  PhD Saša Svetina  Medical sciences  Retired researcher  2022 - 2023  556 
36.  54709  Marin Šako  Natural sciences and mathematics  Junior researcher  2022 - 2023 
37.  54463  Rok Štanc  Natural sciences and mathematics  Junior researcher  2022 - 2023  13 
38.  39231  PhD Vadym Tkachuk  Natural sciences and mathematics  Researcher  2022 - 2023 
39.  26467  PhD Uroš Tkalec  Natural sciences and mathematics  Researcher  2022 - 2023  209 
40.  53592  Erika Tomsič  Natural sciences and mathematics  Junior researcher  2022 - 2023 
41.  30998  Marko Tuljak    Technical associate  2022 - 2023 
42.  39934  PhD Jurij Urbančič  Natural sciences and mathematics  Researcher  2022 - 2023  37 
43.  53816  PhD Horacio Andres Vargas Guzman  Natural sciences and mathematics  Researcher  2022  63 
44.  57913  Domen Vaupotić    Researcher  2023 
45.  13355  PhD Nataša Vaupotič  Natural sciences and mathematics  Researcher  2022 - 2023  285 
46.  26234  PhD Špela Zemljič Jokhadar  Medical sciences  Researcher  2022 - 2023  51 
47.  13415  PhD Primož Ziherl  Natural sciences and mathematics  Head  2022 - 2023  334 
48.  52033  PhD Jan Zmazek  Natural sciences and mathematics  Junior researcher  2022  24 
49.  01068  PhD Boštjan Žekš  Medical sciences  Retired researcher  2022 - 2023  644 
Organisations (6)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0106  Jožef Stefan Institute  Ljubljana  5051606000  87,078 
2.  0381  University of Ljubljana, Faculty of Medicine  Ljubljana  1627066  45,622 
3.  0588  University of Ljubljana, Faculty of Education  Ljubljana  1627082  31,918 
4.  1540  University of Nova Gorica  Nova Gorica  5920884000  13,679 
5.  1554  University of Ljubljana, Faculty of Mathematics and Physics  Ljubljana  1627007  33,279 
6.  2547  University of Maribor, Faculty of natural sciences and mathematics  Maribor  5089638051  17,650 
The program Biophysics of polymers, membranes, colloids, gels and cells is the key national research unit working in biophysics and covering a series of experimental and theoretical themes ranging from the macromolecular scale to tissues and organisms, which are complemented by selected topics in soft-condensed-matter physics and in materials science. The proposed program will primarily address the open basic problems in biophysics such as charge regulation in proteins, hydration interactions of biological membranes, thermodynamics of enzymatic networks, and the response of cells to nanoparticles but it will also deal with topics of potential relevance for biomedical applications and health care such as signaling processes in pancreatic cells related to the type 2 diabetes and the metabolism of breast cancer cells. The 16 topics are grouped into 4 workpackages entitled Soft biomaterials, Biological macromolecules, Vesicles, cells, and tissues, and Signaling pathways and metabolism. The fundamental-science core of the program will be combined with applied and clinical studies to be performed in collaboration with R&D departments of partner high-technology companies and hospitals, respectively. Both theoretical and experimental topics include several methodological projects, e.g., the development of computer code for the modeling of epithelial tissues and microfluidic encapsulation of colloidal particles in droplets. Consisting of established experts as well as of junior researchers, the research program comprises groups from the Jožef Stefan Institute, University of Ljubljana, University of Maribor, and University of Nova Gorica. Their scientific excellence is witnessed by a number of publications in high-impact journals including Nature, Advanced Materials, Nature Chemistry, Proceedings of the National Academy of Sciences USA, etc. Many members of the program also work as professors and teaching assistants at the aforementioned universities. In charge of over 70 courses at all three cycles, they contribute to the development of higher education in Slovenia. Equally important is their engagement as advisors to MS and PhD students and in the many projects dedicated to the popularization of science. Members of the program maintain close ties with a number of groups and laboratories worldwide, collaborating with researchers from Austria, Chile, Croatia, Germany, France, Italy, Japan, The Netherlands, Poland, South Korea, Spain, Sweden, UK, and USA. They also participate in several European and other international networks as well as in many bilateral projects, co-organize scientific meetings and summer schools, serve as visiting professors abroad and as editors and board members of international journals, and write monographs and textbooks. The program is the backbone of biophysics research in Slovenia and a productive and stimulating environment both for researchers and students involved as well as for others working or interested in the field.
Significance for science
The proposed research program is closely integrated into contemporary physics, biophysics and medicine both at the basic and at the applied as well as clinical level. The program consists of four workpackages entitled Soft biomaterials, Biological macromolecules, Vesicles, cells and tissues, and Signaling and metabolism; the workpackages are labeled A through D. Each workpackage contains several intertwined studies, which relate theoretical concepts to practical issues ranging from the understanding of water cavitation in plants and the use of low-dimensional materials as an alternative approach to miniaturization of electronic components to a detailed insight into the mechanisms of the onset of diabetes. At the same time, a number of proposed projects are partly methodological, contributing to the development of theoretical and experimental techniques or computational models; some of them are relevant from the clinical point of view. Workpackage A, which includes topics in soft-condensed-matter physics as well as in materials science, nicely reflects the aforementioned structure. Theoretical studies of the transfer of hierarchical order in new liquid-crystalline materials from the nanoscopic to the microscopic scale will serve as a model of this effect in complex biological molecules. This purely physical challenge will be complemented by characterization of liquid-crystalline phases containing continuous networks, which will allow the use of these materials in drug delivery, organic electronic devices, energy conversion, etc. Liquid crystals are also the basis of dynamically responsive materials to be developed by members of the program using droplet microfluidics, optofluidic encapsulation, and formation of complex emulsions combined with manipulation with laser tweezers, temperature gradients, and microstructured surfaces. These processes will be employed in the design of anisotropically wetted smart surfaces as well as microfluidic and optical sensors sensitive to mechanical, chemical, and biomolecular changes. Also oriented towards applications will be experimental studies of 2D heterostructures relevant for sensor applications. Members of the program will elucidate the dependence of charge transport on the modulation of the reciprocal lattice and on the charge carriers at the interfaces of 2D heterostructures. This is a new approach towards the understanding of these materials, and the expected results will constitute a platform for their application in the next-generation electronic devices. On the other hand, investigations of hydration interactions and wetting will be mainly theoretical, addressing fundamental quantities and phenomena such as a contact angle, adhesion energy, and friction, which are essential for materials science and many technologies. This also applies to the research of biological systems at negative pressures, which is relevant for the vascular transport system in plants and for technological applications such as sonoporation and lithotripsy. On the other hand, studies of interactions between deformable nanocolloidal particles will advance the theoretical understanding of the topic, addressing the contact problem; also theoretical will be the proposed investigations of quasicrystals and hyperuniformity. The other three workpackages too are characterized by basic, methodological, and applied topics. Workpackage B, which will deal with the electrostatic properties of proteins and DNA, the structure of viral capsids, and the secondary structure of RNA, is mostly fundamental. Workpackage C is characterized by a distinct methodological approach because it involves the development of a vertex model used by members of the program to explore structures and processes in epithelial tissues within a mechanistic framework; one of the tasks will be to accelerate the model using machine learning. Apart from employing it in theoretical problems such as the in-depth analysis of mechanics of the early embryonic development of the fruit fly as well as the physical description of organoids, members of the program will make their implementation of the vertex model publicly available as an open-source code. A significant part of the program, especially Workpackage D, connects basic biophysics concepts to applied biomedicine. By studying the energy and signaling processes associated with glucagon secretion, members of the program will examine the biophysical mechanisms of pancreatic alpha cells. This will contribute to the understanding of type 2 diabetes. Based on the principle of maximum entropy production, investigations of the function of enzymes, enzyme networks, and signaling pathways will be used to analyze the impact of nutraceutics with anti-inflammatory action as potential substitutes for NSAIDs. Practical clinical results may result from the study of changes in the metabolic pathways in cancer, especially breast cancer; also studied will be the metabolically induced detachment of cancer cells. The same holds for the development of a new microfluidic method that will allow an accurate time-dependent analysis of the response of single cells and synthetic vesicles to therapeutic agents. Members of the program will also study active substances whose function is associated with a nonspecific interaction with the cell membrane, e.g., antifungals used against spore parasites and proteins from the NLP family involved in infections of the most important crops. Finally, some of the proposed topics relate to questions of the origin of life billions of years ago, where one of the key steps was the separation of the cell from its environment. Selected aspects of the origin of life can be captured by synthetic vesicles, which can divide and aggregate into clusters under appropriate laboratory conditions. A detailed understanding of these processes will also contribute to a deeper insight into the mechanics of cell division and into the structure of early-stage embryos.
Significance for the country
The research program P1-0055 brings together experts in biophysics from the Jozef Stefan Institute and three Slovenian universities - the University of Ljubljana, the University of Maribor, and the University of Nova Gorica - thereby ensuring the continuing active role of the country in this important and rapidly developing field. With their fundamental as well as applied results, members of the program create new knowledge at all levels of biological systems from molecules to cells and tissues as well as in the field of new complex materials, and by sharing their findings they contribute to the social, economical, and cultural progress of Slovenia. As one of the most important research groups in biophysics and soft matter physics in the country, the program is of vital importance for the development of Slovenia primarily because of the expertise of its members, some of them being the sole experts in their respective fields in the country. Many research topics in these fields exist and prosper in Slovenia because they were initiated by members of the program; this applies to, e.g., organic semiconductors, physical virology, mechanics of cells and tissues, and analysis of dynamic systems in biomedicine. Members of the program collaborate with many researchers from renowned universities and laboratories and with their close ties worldwide they contribute to the internationalization of the science community in Slovenia. They also work closely with several expatriate scientists, helping them to share the knowledge acquired abroad with researchers from Slovenia. The high level of the research results of the program is evidenced, among other things, by publications in the most prestigious journals and lectures given at top international scientific meetings. The second key element of the research program with a broad impact on the society is the transfer of knowledge to students. Their expert knowledge allows the members of the program to hold specialized courses that are essential for high-quality and contemporary second- and third-cycle study programs. Members of the program are in charge of about 70 courses at all levels at the aforementioned universities and are thus very important for the higher education in Slovenia. Several members of the program lectured at universities abroad as visiting professors and researchers, and essentially all groups within the program hosted short- and long-term international students. Many research topics covered by the members of the program are routinely included in the various physics courses as well as in those for students of medicine, biology, health sciences, ecology, and bioinformatics and in the continuing professional development of elementary and high-school teachers. In addition to teaching, writing textbooks and lecture notes, a very important segment of the work carried out within the program is the supervision of students' theses at all cycles; the extent of this work is best illustrated by the 35 PhD theses completed under the supervision of the members of the program between 2010 and 2021. A part of activities within the program includes research in education and didactics, which are very important for the development of modern knowledge-based society. In addition to new approaches to teaching physics, members of the program also explore the opportunities to integrate research-related contemporary topics of physics, such as liquid crystals, into elementary- and high-school education. These specific contents not included in the standard curricula are an excellent opportunity to identify talented yet deprived students. In collaboration with both experts in special didactics and practitioners, members of the research program developed a system for identification of such students through suitable experimental activities. In addition to these specific aspects of the transfer of knowledge, they also regularly participate in the popularization of science through lectures and presentations in high schools, science fairs, researchers' night events, physics summer camps, open door days, radio and television shows, presence in printed and web-based media, etc. With these activities, members of the program advance the public awareness of science and promote the improvement of the quality of life through research; during the COVID-19 pandemic, they described the physical principles of the droplet and aerosol transmission of infections in both lectures for the scientific audience and in articles for the general public. Through courses taught and papers written in Slovenian, members of the program continually contribute to the development of the scientific terminology in Slovenian in their respective fields. Even though the program is focused chiefly on basic research, some of the results obtained are relevant for the industry and healthcare based in Slovenia as evidenced by numerous projects carried out for business enterprises and healthcare institutions. During the past period, members of the program worked on joint projects with high-tech companies such as Lek, Krka, Acies Bio, Kolektor Sikom, Vitiva, and Aresis. They also hold several domestic and foreign patents. Also important is their collaboration with hospitals, community health centers, the National Laboratory of Health, Environment and Food, and the Health Insurance Institute of Slovenia, which involves various areas of expertise. Finally, a long-term impact on the development of society is expected from the participation of members of the program in the Graphene Flagship as one of the strategic projects of the European Commission. The involvement of the senior researchers and students in this project is important firstly because of the expected new scientific results and secondly because this project allows them to better disseminate the knowledge in the field of quantum technologies at the national level.
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