Biophysical Chemistry: Diffusion and reactions in a crowded environment

Research group no. 31

Biophysical Chemistry: Diffusion and reactions in a crowded environment

Group leader

dr hab. Anna Ochab-Marcinek

Research topics

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

Members

  • dr Jakub Jędrak
  • mgr Marcin Rubin

Research

Evolution of gene regulation as a stochastic process: Savageau's demand theory, cost of regulation and noise Sonata Bis project no. 2016/22/E/ST2/00558, financed by the National Science Centre. 

The “demand theory”, formulated by the M.A. Savageau in the 70s, explains the evolution of positive or negative gene regulation by the frequency of demand for a given protein and sensitivity of genes to mutations. However, in recent years, with the advent of systems biology and its tools, new studies began to appear, questioning the universality of the theory and extending it with new criteria. Since even a genetically uniform population of cells is subject to random fluctuations in gene expression, a phenotypic diversity exists in such a population. We want to see how taking into account the costs of regulation and random fluctuations in the concentrations of transcription factor complements the classic Savageau’s demand rules? The project is theoretical – we use the tools of statistical physics and the theory of stochastic processes – but it may deliver experimentally testable predictions and can encourage biologists to carry out new types of evolutionary experiments, focusing on the role of randomness in gene expression. In the long term, understanding the evolution of phenotypic diversity is crucial in the struggle against bacterial resistance to antibiotics, one of the most pressing problems of modern medicine. 

Cooperation

Dr. Bartłomiej Wacław, The University of Edinburgh

Modeling of biological evolution. Stochastic gene expression.

Financing

NCN Sonata Bis: Evolution of gene regulation as a stochastic process: Savageau's demand theory, cost of regulation and noise (15.5.2017-14.7.2022)

http://groups.ichf.edu.pl/ochab/funding/view

Iuventus Plus: Theoretical study of conditions for precise gene regulation in a 2-gene cascade with autoregulation (7.2013-7.2015)

http://groups.ichf.edu.pl/ochab/funding/view

NCN Sonata: Transition from nano- to macroviscosity in diffusion of nanoparticles in a crowded environment: Theoretical and experimental study of the depletion layer effect (12.2011- 12.2014)

http://groups.ichf.edu.pl/ochab/funding/view