Seminarium z fizyki biologicznej i bioinformatyki
2014/2015 | 2015/2016 | 2017/2018 | 2018/2019 | 2019/2020 | 2020/2021 | 2021/2022 | 2022/2023 | 2023/2024 | 2024/2025 | 2025/2026 | 2026/2027 | Strona własna seminarium
2026-06-24 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15 
Prof. Włodzimierz Mandecki (Rutgers University - New Jersey Medical School Newark, NJ, U.S.A.)Discovering antibiotics that block EF-Tu-dependent steps of bacterial protein synthesis
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
There is a critical need for new antibiotics to treat bacterial infections caused by pathogens that are resistant to many, if not all, currently available drugs. Here, we present a method for identifying a prospective new antibiotic by first developing a dedicated assay and then using it for high throughput screening of a chemical compound library. The screen was designed to detect inhibition of the formation of the “ternary complex,” a structure essential for bacterial protein synthesis in all bacteria, composed of elongation factor Tu (EF-Tu), aminoacyl-tRNA, and GTP. The inhibitory compound, designated MGC-10, was effective against all Gram positive bacteria tested, including a wide variety of methicillin resistant Staphylococcus aureus (MRSA) strains. Although apparently too toxic for systemic use, the compound was safe and effective for topical treatment of skin infections in a mouse model. No resistance to the compound has been detected thus far, suggesting strong potential for treating infections caused by pathogens resistant to existing antibiotics.
2026-06-10 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Dr Tomasz Włodarski (Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw)Co-translational protein folding in the light of ribosome evolution
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2026-06-03 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. Andrzej Górecki (Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków)Gene Regulation as a Game of Transient Interactions: From Structural Determinism to Protein Quinary Structure
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
Classical structural biology explains protein function primarily throughstable and well-defined molecular structures. While this paradigm successfully describes many biological processes, increasing evidence suggests that the cellular context in which proteins operate can be equally important in determining their activity. These effects appear to be particularly important in the regulation of gene expression in eukaryotic cells. Biochemical and biophysical studies indicate that complex regulatory phenomena can emerge from transient interactions, structuralheterogeneity, and cooperative network behavior, pointing toward a moredynamic view of cellular organization associated with protein quinary structure.Many transcription factors contain intrinsically disordered regions(IDRs) that mediate interactions with DNA, proteins, and the surrounding cellular environment. In such systems, regulation emerges not from single stable complexes but from the collective behavior of dynamically reorganizing interaction networks. Particular attention will be given to the transcription factors YY1 and YY2, whose intrinsically disordered regions enable flexible interactions with DNA and protein partners, contributing to context-dependent control of gene expression.
2026-05-20 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Stanisław Żukowski (IFT, WF, UW, Laboratoire Matiere et Systemes Complexes, Universite Paris Cite, Paris, France)Morphogenesis of transport networks in nature: from capillaries to jellyfish canals
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2026-05-06 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. Wiktor Koźmiński (Biological and Chemical Research Centre University of Warsaw)High dimensional and high resolution NMR methods for studies of intrinsically disordered proteins
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2026-04-22 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. Artur Bednarkiewicz (Institute of Low Temperature and Structure Research, Polish Academy of Sciences Wroclaw)Photon avalanche and upconversion phenomena for novel sensing and bioimaging
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
ABSTRACTPhoton avalanche (PA) is a highly nonlinear optical phenomenon firstdiscovered in 1979, originally investigated in bulk crystals at cryogenic temperatures for mid-infrared photon detection and upconversion lasers. It is initiated when photon absorption triggers a cascade of excited-state absorption (ESA) and energy transfer processes, forming a positive feedback loop that rapidly amplifies emission. A defining feature of PA is a sharp excitation power threshold, above which the luminescence intensity increases dramatically. Beyond this threshold, the emission intensity (IE) follows a power-law dependence on excitation power (IP), IE=(IP)^S,with an exceptionally large nonlinearity index S exceeding 10 and sometimes reaching several hundred. The process exhibits efficient anti-Stokes emission and a characteristic S-shaped dependence of emission intensity on excitation power density [1]. Achieving PA requires stringent conditions, including resonant ESA between excited states and an ESA cross section much larger than ground-state absorption. Equally critical is efficient cross-relaxation between lanthanide ions, which multiplies the population of intermediate states and sustains the avalanche process. Recentdemonstrations of PA in nano- and micro-scale materials, particularlyTm^3+-doped low-phonon hosts, have opened new opportunities for ultrasensitive sensing and advanced photonic technologies. During the talk, the basics of PA will be presented, likewise the novel concepts and demonstrations of superresolution imaging [2,3,4], and ultrasensitizesensing [1,5,6]. Some new directions and challenges will be indicated towards better (lower threshold, controlled non-linearity) PA nano & micro particles and layers.References 1. M. Szalkowski, A. Kotulska, M. Dudek, Z. Korczak, M. Majak, Ł.Marciniak, M. Misiak, K. Prorok, A. Skripka, P. J. Schuck, E. M. Chan, A.Bednarkiewicz, et al.,Chem. Soc. Rev. 54, 983 (2025). 2. Artur Bednarkiewicz, Emory M.-Y. Chan, Agata M. Kotulska, ŁukaszMarciniak, Katarzyna Prorok, et al., Nanoscale Horiz. 4, 706 (2019). 3. Lee, E. Xu, Y. Liu, A. Teitelboim, K. Yao, A. Fernandez-Bravo, A. Kotulska, S. H. Nam, Y. D. Suh, A. Bednarkiewicz, B. E. Cohen, E. M. Chan, P. J. Schuck, et al., Nature 592, 554 (2021). 4. S. Karmegam, M. Szalkowski, M. Misiak, K. Prorok, D. Szymański,A. Bednarkiewicz, et al., arXiv:2507.14667 (2025). 5. Bednarkiewicz, E. M. Chan, K. Prorok, et al., Nanoscale Adv. 2, 4863 (2020). 6. M. Majak, M. Misiak, A. Bednarkiewicz, et al., Mater. Horiz. 11, 4791 (2024).
2026-04-08 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Dr Ewelina Małecka (Laboratory of Single-Molecule Biophysics International Institute of Molecular and Cell Biology Warsaw)Choreography of RNA-protein interactions for gene regulation at single-molecule level
link do spotkania:https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2026-03-25 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Dr hab. inż. Piotr Batys, prof. IKiFP PAN (Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Kraków)From Molecular Design to Material Function: Predictive Engineering of Phase-Separating Protein Biomaterials
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2026-03-11 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. Pavlo O. Dral (Institute of Physics, Nicolaus Copernicus University in Toruń, Poland and Department of Chemistry, Xiamen University, China)Autonomous AI agents for performing AI-driven computational chemistry simulations online
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2026-01-14 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
dr hab. Szymon Kaczanowski (Institute of Biochemistry and Biophysics, Polish Academy of Sciences)The Evolutionary History of Apoptosis: The Predator – Mitochondrial Prey Hypothesis
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2025-12-17 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. Krzysztof Szalewicz (University of Delaware, Department of Physics & Astronomy, Newark, USA)"From the Schrödinger equation to crystal structure and biomolecular predictions"
Link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
In 1928, Dirac correctly foresaw that the main future goal of physicsis finding approximate methods for solving Schrödinger's equation.The current status of first-principles quantum mechanical methodsapplied to the modelling of interactions between molecules will bepresented, with particular emphasis on symmetry-adapted perturbationtheory. However, to model condensed matter, including biosystems,one has to fit ab initio data by simple functions of interatomicseparations called force fields. A machine-learning program calledautoPES performs such fits purely automatically, opening new avenuesfor investigating condensed phases. Applications for predictingcrystal structures will be presented.
2025-12-03 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. dr hab. Bogdan Lesyng (Division of Biophysics and Centre for Machine Learning, Faculty of Physics, University of Warsaw)How mathematical and computational theories and models in the natural sciences evolve over time
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
There are significant analogies between the processes of Darwinian biological evolution and the evolution of physical/chemical theories and/or models over time. Evolutionary genealogical, hierarchical, and/or flowchart diagrams of the development of various fields of knowledge have been created and analysed using AI methods. For example, the structure of evolutionary trees characterizing molecular modelling methods can be examined. This is particularly useful when entering a new field of research.This type of analysis can also prove effective in teaching, as it allows for more effective transfer of knowledge to students.
2025-11-19 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. Joanna Olesiak-Bańska (Institute of Advanced Materials, Wroclaw University of Science and Technology)Atomically precise Au/Ag nanoclusters as NIR luminescent markers for in vivo imaging
Link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2025-11-12 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
Prof. Nevena Ilieva (Institute of Information and Communication Technologies, Department of Scientific Computations Bulgarian Academy of Sciences, Sofia, Bulgaria)From Viral Protein to Antiviral Lead: an AI-Assisted in Silico Design Journey
link do spotkania: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
The COVID-19 pandemic has underscored the role of structural andcomputational biophysics in antiviral discovery. In this talk, I will present an in silico design workflow that connects viral protein characterization, molecular dynamics simulations, and AI-based modeling. We focus on two SARS-CoV-2 proteins – the multifunctional helicase NSP13 and the interferon antagonist ORF6 – as potential drug targets. I will discuss computationally identified and experimentally confirmed inhibitory motifs and introduce the concepts of protein aptamers and cyclotides as promising scaffolds for peptide-based antivirals. Using molecular dynamics simulations and a convolutional neural network (CNN) trained for interaction assessment, we have explored the feasibility of grafting viral peptide motifs onto cyclotide scaffolds. Although this approach is still under experimental validation, the results demonstrate how AI-enhanced In-silico methods can transform structural insights into rational antiviral design strategies.
2025-10-22 (Środa)
Zapraszamy do sali D, IFPAN, al. Lotników 32/46 o godzinie 15:15
dr hab. Ewelina Lipiec, prof. UJ (Katedra Fizyki Nanostruktur i Nanotechnologii Instytut Fizyki im. Mariana Smoluchowskiego Wydział Fizyki, Astronomii i Informatyki Stosowanej Uniwersytet Jagielloński w Krakowie)Mind the Gap! Plasmonic nanocavity for spectroscopic trapping of local molecular rearrangements in biomolecules
link do seminarium: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
2025-10-08 (Środa)
Zapraszamy do Audytorium, IFPAN, al. Lotników 32/46 o godzinie 15:15
Dr Jer-Lai Kuo (Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan)Neural network-assisted first-principles exploration on the conformational space of peptides and saccharides
Link to the meeting: https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09
Sampling of the conformational space of peptides and saccharides with first-principle accuracy is critical as such a database provide a solid base to interpret experimental measurements such as Infrared photo-dissociation (IRPD) spectroscopy, ion mobility spectrometry (IMS), or collision-induced dissociation (CID). The conformational space of both peptides and saccharides are highly flexible, in which the distinct conformers of mono- and di-saccharide is estimated to be in the order of 103 and 106, respectively. To efficiently explore the diverse conformational space of saccharide without losing accuracy, we developed a multi-level sampling scheme integrating semi-empirical models, density function theory (DFT) and neural network potential (NNP) that can be routinely be applied to study di-saccharides and hexa-peptides. Preliminary results, shown on the right, demonstrate the decent agreement between experimental IRPD spectra and IR absorption simulated based on low-energy conformers of sodiated Gal-14GlcNAc at DFT. We are optimistic that the combination of theory and gas-phase experimental can provide a new dimension into explore the structures of these bio-molecules.