ZB 31 - Biophysical Chemistry Group (A.Ochab)

Anna Ochab-Marcinek, Ph. D. (dr hab.)

Principal Investigator                                 ochab[AT]ichf.edu.pl ↝ CV [pdf] ↝ Research interests ↝ COVID-19 ↝ Publications

↝ GitHub ↝ Patents ↝ Popular science ↝ Old home page

↝ Google Scholar ↝ ORCID ↝ ResearcherID ↝ Publons

 

 

 

Research interests
 

• Modeling of biological evolution
• Stochastic gene expression
• Diffusion in a crowded environment

 

 

 

 

 

 

Publications

1. J. Jędrak, M. Rubin, A. Ochab-Marcinek, Generalization of Powell's results to population out of steady state, Physical Review E 108 (2), 024405 (2023) [arxiv preprint]
2. J. Jędrak, A. Ochab-Marcinek, Contributions to the 'noise floor' in gene expression in a population of dividing cells, Scientific Reports, 10, 13533 (2020
3. A. Ochab-Marcinek, M. Kwiatkowski, J. Jędrak, Exactly solvable model of gene expression in proliferating bacterial cell population with stochastic protein bursts and protein partitioning, Phys. Rev. E, 99 (2019) 042416 [arxiv preprint]
4. A. Ochab-Marcinek, J. Jędrak, M. Tabaka, Hill kinetics as a noise filter: The role of transcription factor autoregulation in gene cascades, Phys. Chem. Chem. Phys., 2017, 19, 22580-22591
5. G. Angulo, J. Jedrak, A. Ochab-Marcinek, P. Pasitsuparoad, C. Radzewicz, P. Wnuk, A. Rosspeintner, How good is the generalized Langevin equation to describe the dynamics of photo-induced electron transfer in fluid solution? , J. Chem. Phys. 146 (2017) 244505 [arxiv preprint]
6. J. Jędrak, A. Ochab-Marcinek, Influence of gene copy number on self-regulated gene expression, J. Theor. Biol., 408 (2016) 222 [arxiv preprint]
7. J. Jędrak, A. Ochab-Marcinek, Time-dependent solutions for a stochastic model of gene expression with molecule production in the form of a compound Poisson process, Phys. Rev. E 94 (3) (2016) 032401 [arxiv preprint]
8. T. Kalwarczyk, K. Sozanski, A. Ochab-Marcinek, J. Szymanski, M. Tabaka, S. Hou, R. Holyst, Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model, 2015, Advances in Colloid and Interface Science, 2015, 223, 55-63.
9. A. Ochab-Marcinek, M. Tabaka, Transcriptional leakage versus noise: A simple mechanism of conversion between binary and graded response in autoregulated genes, Phys. Rev. E, 2015, 91(1), 012704 [arxiv preprint]
10. K. Sozanski, A. Wisniewska, T. Piasecki, K. Waszczuk, A. Ochab-Marcinek, T. Gotszalk,R. Holyst, Depletion Layer in Polymer Solutions at an Interface Oscillating at the Subnano-to Submicrometer Scale, Soft Matter 2014, 10, 7762-7768
    [ free accepted manuscript - please note that according to the RSC license, this pdf copy may not be further made available or distributed]
11. T.K.Piskorz, A. Ochab-Marcinek, A Universal Model of Restricted Diffusion for Fluorescence Correlation Spectroscopy, J. Phys. Chem. B, 2014, 118 (18), 4906–4912
12. A. Lewandrowska, A. Majcher, A. Ochab-Marcinek, M. Tabaka, R. Hołyst, Taylor Dispersion Analysis in Coiled Capillaries at High Flow Rates, Anal. Chem., 2013, 85 (8), 4051–4056
13. A. Ochab-Marcinek, S.A. Wieczorek, N. Ziębacz, R. Hołyst, The effect of depletion layer on diffusion of nanoparticles in solutions of flexible and polydisperse polymers , Soft Matter 2012, 8, 11173-11179
    [please note that according to the RSC license, this pdf copy may not be further made available or distributed]
14. A. Ochab-Marcinek, R. Hołyst, Scale-dependent diffusion of spheres in solutions of flexible and rigid polymers: mean square displacement and autocorrelation function for FCS and DLS measurements , Soft Matter 2011, 7, 7366-7374
    [please note that according to the RSC license, this pdf copy may not be further made available or distributed]
15. A. Ochab-Marcinek, M. Tabaka, Bimodal gene expression in noncooperative regulatory systems , PNAS 107(51) (2010) 22096-22101
16. A. Ochab-Marcinek, Extrinsic noise passing through a Michaelis-Menten reaction: A universal response of a genetic switch, J. Theor. Biol. 263(4) (2010) 510-520 [arxiv preprint]
17. A. Ochab-Marcinek, E. Gudowska-Nowak, E. Nasonova, S. Ritter, Modelling radiation-induced cell cycle delays, Rad. Env. Biophys. 48(4) (2009) 361 [arxiv preprint, the original publication is available at www.springerlink.com]
18. A. Ochab-Marcinek, G. Schmid, I. Goychuk, P. Hanggi, Noise-assisted spike propagation in myelinated neurons, Phys. Rev. E 79, 011904 (2009) [arxiv preprint]
19. A. Fiasconaro, A. Ochab-Marcinek, B. Spagnolo, E. Gudowska-Nowak, Monitoring noise-resonant effects in cancer growth influenced by external fluctuations and periodic treatment, Eur. Phys. J. B 65, 435-442 (2008) [arxiv preprint]
20. Anna Ochab-Marcinek, Predicting the asymmetric response of a genetic switch to noise, J. Theor. Biol. 254 (2008) 37-44 [arxiv preprint]
21. B. Spagnolo, A.A. Dubkov, A.L. Pankratov, E.V. Pankratova, A. Fiasconaro, A. Ochab-Marcinek Lifetime of Metastable States and Suppression of Noise in Interdisciplinary Physical Models. Acta Physica Polonica B 38(5) 2007, 1925.
22. Anna Ochab-Marcinek, Alessandro Fiasconaro, Ewa Gudowska-Nowak, Bernardo Spagnolo, Coexistence of resonant activation and noise-enhanced stability in a model of tumor-host interaction: Statistics of extinction times. Acta Physica Polonica B 37(5) 2006, 1651.
23. Alessandro Fiasconaro, Bernardo Spagnolo, Anna Ochab-Marcinek, Ewa Gudowska- Nowak, Co-occurrence of resonant activation and noise-enhanced stability in a model of cancer growth in the presence of immune response. Physical Review E 74, 041904 (2006)
    [arxiv preprint]
24. Anna Ochab-Marcinek: Transient pattern formation in a stochastic model of cancer growth, Fluctuation and Noise Letters 5(2) (2005) L331
    [arxiv preprint]
25. Anna Ochab-Marcinek: Pattern formation in a stochastic model of cancer growth , Acta Physica Polonica B 36(6) (2005) 1963
    [arxiv preprint]
26. Anna Ochab-Marcinek, Ewa Gudowska-Nowak: Population growth and control in stochastic models of cancer development, Physica A, 343 (2004) 557-572
    [arxiv preprint]

 

COVID-19 Advisory Team to the President of the Polish Academy of Sciences

 

From 30 Jun 2020 until 31 Dec 2022, I was a member of the interdisciplinary COVID-19 Advisory Team affiliated with the President of the Polish Academy of Sciences. Our task was to monitor the course of the COVID-19 epidemic in Poland, analyze and predict its possible scenarios and put forward recommendations. We also developed contacts with similar teams in other countries to exchange experiences with them.

 

Our position statements

Archive of my epidemiological data analyses. See also GitHub.

 

Publications (non peer-reviewed):

1. J. Duszyński, A. Afelt, A. Ochab-Marcinek, R. Owczuk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Zrozumieć COVID-19, ACADEMIA - magazyn Polskiej Akademii Nauk 4 (64) 2020 pp. 1-80, DOI:10.24425/academiaPAN.2020.136169

2. J. Duszyński, A. Afelt, A. Ochab-Marcinek, R. Owczuk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Understanding COVID-19, ACADEMIA - The magazine of the Polish Academy of Sciences 4 (68) 2020 pp. 1-80, DOI:10.24425/academiaPAS.2020.136172 

3. J. Duszyński, A. Afelt, M. Kossowska, A. Ochab-Marcinek, R. Owczuk, W. Paczos, A. Plater-Zyberk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Kroniki Pandemii: lata 2020-2021, ACADEMIA - magazyn Polskiej Akademii Nauk 4(68) 2021 pp. 1-118, DOI:10.24425/academiaPAN.2021.140621 

4. J. Duszyński, A. Afelt, M. Kossowska, A. Ochab-Marcinek, R. Owczuk, W. Paczos, A. Plater-Zyberk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Chronicles of a Pandemic, ACADEMIA - The magazine of the Polish Academy of Sciences 4(72) 2021 pp. 1-120

 

GitHub

• anuszka/COVID-19-MZ_GOV_PL: COVID-19 statistics for Poland, captured from Polish Health Ministry's Twitter.
  My plots and comments on these data are here: http://soft.ichf.edu.pl/ochab/coronavirus_poland/
   

Patents

• A. Lewandrowska, A. Majcher, M. Tabaka, A. Ochab-Marcinek, R. Hołyst Sposób wyznaczania współczynnika dyfuzji D substancji chemicznej w buforze TRIS (Method for determination of diffusion coefficient D of a chemical substance in TRIS buffer). Patent no. 220250 (Polish Patent Office), granted 4.12.2014

 

Popular science

 

Anna Ochab-Marcinek, Porządek z przypadku, Academia, magazine of the Polish Academy of Sciences, 4/11(28)
Radio interview [Polish]: Wieczor Odkrywcow, Polskie Radio 1, 9.7.2011
Radio interview [Polish]: Radiowa Akademia Nauk, Radio TOK FM, 2.3.2011

 

Popular science articles for Tygodnik Powszechny weekly:

• Anna Ochab-Marcinek, Klucz do komórki, Tygodnik Powszechny Nr 2 (3209), 9.1.2011

• Anna Ochab-Marcinek, Geniusz z Wrocławia, Tygodnik Powszechny Nr 1-2 (3104-05), 4-11.1.2009

• Anna Ochab-Marcinek, Patent hochsztaplera, Tygodnik Powszechny 50 (3101) 14.12.2008

• Anna Ochab-Marcinek, Doktorat z telepatii, Tygodnik Powszechny 45 (3096) 9.11.2008

• Anna Ochab-Marcinek, Więcej niż mrówek, Tygodnik Powszechny 37 (3088) 14.9.2008

 

Popular science blogs

• Blog Świat: Jak To Działa? (World: How Does It Work?) for Tygodnik Powszechny.

• Blog Będąc młodym Fizykiem (Being a Young Physicist), a collection of the most interesting pseudo-science ideas.