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Completed project: 

12.2011- 12.2014: National Science Center SONATA grant no. 2011/01/D/ST3/00751
Transition from nano- to macroviscosity in diffusion of nanoparticles in a crowded environment: Theoretical and experimental study of the depletion layer effect

Gene expression strongly depends on the rate constants of biochemical reactions, such as e.g. transcription factor + DNA. A small variation in these rates may dramatically change the gene expression. Therefore, in order to design genetic circuits having desired properties, biotechnologists have to know exactly the rates of reactions that control gene expression. In biochemistry, a standard reaction rate analysis is usually done in vitro, in a buffer of viscosity of water. However, in vivo, in a crowded environment of high viscosity, biochemical reactions are usually limited by diffusion, and their rates may differ by several orders of magnitude from those expected based on the standard measurements. Moreover, many biochemical reactions in living cells are diffusion-limited. If the diffusion of molecules in a crowded environment differs from that expected based od in vitro experiments, then also the rates of biochemical reactions may be quite different from in vitro predictions.

In this project, we study (both theoretically and experimentally) the transition from the nanoscopic to macroscopic diffusion in a crowded environment. In particular, we study the effect of the less crowded depletion layer around the diffusing nanoparticle. The depletion layer affects the speed of diffusion in different length scales: The motion of the nanoparticle is faster within the less crowded layer and slower on longer distances. We want to experimentally measure the depletion layer thickness, to understand theoretically the dependence of that thickness on the particle size and other factors. Next, we want to understand how the rates of biochemical reactions, especially those involved in gene regulation, are affected by this non-uniform diffusion.

The experimental methods we use are: dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS).


Scientific papers published as the result of the project:
  1. 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.
  2. 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]
  3. 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
  4. J. Jędrak Cluster-size distribution in the autocatalytic growth model, Physical Review E 89.5 (2014): 052122 [ArXiV preprint]
  5. 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
  6. 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]