CV

Education

• PhD in Chemistry, Institute of Physical Chemistry, Polish Academy of Sciences, 2018-2023
• Postgraduate Diploma, Software Development Methods, AGH University of Science and Technology, 2017-2018
• PhD in Chemistry, Faculty of Chemistry, Jagiellonian University, 2016-2018 (abandoned)
• MSc in Chemistry, Faculty of Chemistry, Jagiellonian University, 2014-2016
• BSc in Chemistry, Faculty of Chemistry, Silesian University, 2011-2014

Work experience

• 2023-present: Postdoctoral Research Associate
  • Scientific Computing and Imaging Institute, University of Utah
  • Principal investigator: Dr. Tamara Carla Bidone
• 2018-2023: Research Assistant
  • Institute of Physical Chemistry, Polish Academy of Sciences
  • Duties included: Brownian dynamics simulations of diffusion and reactions in crowded environments
  • Supervisor: Dr. Svyatoslav Kondrat
• Spring 2017: Trainee
  • School of Chemistry, University of Glasgow
  • Duties included: Implementation of singlet fission model into vibr_cryst program
  • Supervisor: Dr. Anna Stradomska-Szymczak

Skills

• Languages: English (C1), French (A1), Polish (native),
• Programming languages: Python, C, Java
• Version controlling using git,
• clean code, SOLID design principles,
• bash scripts, linux command line, LaTeX,
• Brownian dynamics simulations and data analysis.

Publications

Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation

Wu, J., Dasetty, S., Beckett, D., Wang, Y., Xue, W., Skóra, T., Bidone, T. C., Ferguson, A. L., & Voth, G. A. Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation. bioRxiv 2024.10.10.617682; doi: https://doi.org/10.1101/2024.10.10.617682 (2024)

On the importance of the diffusivity gradient term in Brownian dynamics simulations

Skóra, T. On the importance of the diffusivity gradient term in Brownian dynamics simulations. Biophysical Journal 123, 2638-2640 (2024)

Properties of Coherent Vibrational Wavepackets Critically Depend on the Method of Their Generation

Andrzejak, M., Mazur, G., Musser, A. J., Petelenz, P., & Skóra, T. Properties of Coherent Vibrational Wavepackets Critically Depend on the Method of Their Generation. The Journal of Physical Chemistry C 128, 9837–9846 (2024)

Contributions of the individual domains of αIIbβ3 integrin to its extension: Insights from multiscale modeling

Skóra, T., Joshi, O., Yarema, A., Rabbitt, R. D., & Bidone, T. C. Contributions of the individual domains of αIIbβ3 integrin to its extension: Insights from multiscale modeling. Cytoskeleton 81, 393-408 (2024)

Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds

Raczyłło, E., Gołowicz, D., Skóra, T., Kazimierczuk, K., & Kondrat, S. Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds. Nano Letters 24, 4801–4809 (2024)

Bottom-up coarse-grained model of microtubule dynamics: A bridge between length- and timescales

Skóra, T., Beckett, D., & Bidone, T. C. Bottom-up coarse-grained model of microtubule dynamics: A bridge between length- and timescales. Biophysical Journal 123, 272a (2024)

Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding

Skóra, T., Słyk, E., & Kondrat, S. Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding. The Journal of Physical Chemistry B 127, 7442–7448 (2023)

Crowding-regulated binding of divalent biomolecules

Skóra, T., Janssen, M., Carlson, A., & Kondrat, S. Crowding-regulated binding of divalent biomolecules. Physical Review Letters 130, 258401 (2023)

Diffusion and reactions under crowding: Theory and simulations

Skóra, T. Diffusion and reactions under crowding: Theory and simulations. PhD Thesis (2023)

How macromolecules softness affects diffusion under crowding

Słyk, E., Skóra T., & Kondrat, S. How macromolecules’ softness affects diffusion under crowding. Soft Matter 18, 5366–5370 (2022)

Conformation-changing enzymes and macromolecular crowding

Skóra, T., Popescu, M. N., & Kondrat, S. Conformation-changing enzymes and macromolecular crowding. Physical Chemistry Chemical Physics 23, 9065–9069 (2021)

Soft selection rules for femtosecond Pump–probe vibrational coherence spectroscopy

Andrzejak, M., Mazur, G., Skóra, T., & Petelenz, P. Soft selection rules for femtosecond pump–probe vibrational coherence spectroscopy. The Journal of Physical Chemistry C 124, 23501-23510 (2020)

Macromolecular crowding: how shape and interactions affect diffusion

Skóra, T., Vaghefikia, F., Fitter, J., & Kondrat, S. Macromolecular crowding: how shape and interactions affect diffusion. The Journal of Physical Chemistry B 124, 7537–7543 (2020)

Limitations of generic chromophore concept for femtosecond vibrational coherences

Andrzejak, M., Skóra, T., & Petelenz, P. Limitations of generic chromophore concept for femtosecond vibrational coherences. The Journal of Physical Chemistry C 124, 3529-3535 (2020)

Is vibrational coherence a byproduct of singlet exciton fission?

Andrzejak, M., Skóra, T., & Petelenz, P. Is vibrational coherence a byproduct of singlet exciton fission? The Journal of Physical Chemistry C 123, 91–101 (2018)

Awards

• 2024: Biophysical Society 2024 Annual Meeting Travel Award, Biophysical Society
• 2023: Distinction award for best PhD theses, Academic Computer Centre Cyfronet, AGH University of Krakow
• 2022: Young researchers IPC PAS, Institute of Physical Chemistry, Polish Academy of Sciences
• 2021: Awarded Poster at Microsymposium IPC PAS, Institute of Physical Chemistry, Polish Academy of Sciences

Service and leadership

• Science popularization at the 25th Science Picnic of Polish Radio and the Copernicus Science Center
• Member of Biophysical Society (since 2020)
• Student Scientific Association “Aqua Regia” at the University of Silesia (member 2011-2014; chairman in 2014)