Soft Condensed Matter

Research group no. 10

Soft Condensed Matter

Group leader

prof. dr hab. Robert Hołyst

+48 22 343 3123

rholyst@ichf.edu.pl

Research topics

We analyze biochemical reaction at a single molecule level using spectroscopic methods with single photon counting. We analyze these reactions in vials and in living cells. Additionally we develop new methods in non-equilibrium statistical physics. We also produce SERS substrates.

Members

  • Prof. Robert Hołyst - Team Leader
  • Prof. Anna Maciołek
  • Prof. Andrzej Poniewierski
  • Dr. Karina Kwapiszewska
  • Dr. Tomasz Kalwarczyk
  • Dr. Grzegorz Bubak
  • Dr. Tomasz Andryszewski
  • Dr. Karol Makuch
  • Dr. Paweł Żuk
  • Dr. Jeffrey Everts
  • Dr. Marta Pilz
  • MSc. Paweł Albrycht 
  • Aneta Karpińska, PhD Student
  • Alicja Zgorzelska, PhD Student
  • Karolina Kucharska, PhD Student
  • Sakshi Sareen, PhD Student
  • Adam Kowalski, PhD Student
  • Katarzyna Ulewicz, Student
  • Jarosław Michalski, Student
  • dr Patrycja Haniewicz
  • mgr Huma Jamil
  • mgr Yaroslava Oliinyk
  • mgr Uladzislau Sakalouski
  • Krystyna Pszczółkowska, Administration
  • Kuźma Patrycja, Research Group Coordinator & Lab Manager
See external website

Research

Highlighted papers

  • "Diffusion and flow in complex liquids" Makuch K. et al., Soft Matter 2020
  • "Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines" Kwapiszewska K. et al., The Journal of Physical Chemistry Letters 2020
  • "Comparative analysis of viscosity of complex liquids and cytoplasm of mammalian cells at the nanoscale", Kalwarczyk T. et al., Nano Letters 2011
  • "Diffusion and viscosity in a crowded environment: from nano-to macroscale", Szymanski J. et al., J. Phys. Chem. B 2006
  • "Flux and storage of energy in nonequilibrium stationary states", Holyst R. et al., Phys. Rev. E 2019
  • "A molecular dynamics test of the Hertz–Knudsen equation for evaporating liquids", Holyst R. et al., Soft Matter 2015
  • "Nanoscale transport of energy and mass flux during evaporation of liquid droplets into inert gas: computer simulations and experiments", Holyst R. et al., Soft Matter 2013 
  • "Heat transfer at the nanoscale: Evaporation of nanodroplets" Holyst R. and Litwniewski M., Phys. Rev. Lett. 2008
  • "Three-dimensional space partition based on the first Laplacian eigenvalues in cells", Cybulski O. and Holyst R., Phys. Rev. E 2008
  • "Tiling a plane in a dynamical process and its applications to arrays of quantum dots, drums, and heat transfer", Cybulski O. and Holyst R., Phys. Rev. Lett. 2005

Publications

2021

Richter, Ł., Księżarczyk, K., Paszkowska, K., Janczuk-Richter, M., Niedziółka-Jönsson, J., Gapiński, J., Łoś, M., Hołyst, R., & Paczesny, J.
Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research.
Scientific Reports, https://doi.org/10.1038/s41598-021-86571-x

Everts, J. C., & Ravnik, M.
Ionically Charged Topological Defects in Nematic Fluids.
Physical Review X, https://doi.org/10.1103/PhysRevX.11.011054

Agasty, A., Wisniewska, A., Kalwarczyk, T., Koynov, K., & Holyst, R.
Macroscopic Viscosity of Polymer Solutions from the Nanoscale Analysis.
ACS Appl. Polym. Mater., https://doi.org/10.1021/acsapm.1c00348

Kucharska, K., Pilz, M., Bielec, K., Kalwarczyk, T., Kuźma, P., & Hołyst, R.
Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA.
Molecules, https://doi.org/10.3390/molecules26123748

Kleczewska, N., Sikorski, P. J., Warminska, Z., Markiewicz, L., Kasprzyk, R., Baran, N., Kwapiszewska, K., Karpinska, A., Michalski, J., Holyst, R., Kowalska, J., & Jemielity, J.
Cellular delivery of dinucleotides by conjugation with small molecules: targeting translation initiation for anticancer applications.
Chemical Science, https://doi.org/10.1039/D1SC02143E

Al-Otaibi, J. S., Albrycht, P., Mary, Y. S., Mary, Y. S., & Księżopolska-Gocalska, M.

Concentration-dependent SERS profile of olanzapine on silver and silver-gold metallic substrates.

Chemical Papers, https://doi.org/10.1007/S11696-021-01783-9 

Kalwarczyk, T., Bielec, K., Burdzy, K., & Holyst, R.

Influence of molecular rebindings on the reaction rate of complex formation.

Physical Chemistry Chemical Physics, https://doi.org/10.1039/D1CP02820K

Al-Otaibi, J. S., Albrycht, P., Mary, Y. S., Mary, Y. S., & Księżopolska-Gocalska, M.

Concentration-dependent SERS profile of olanzapine on silver and silver-gold metallic substrates.

Chemical Papers, https://doi.org/10.1007/S11696-021-01783-9

Albrycht, P., Al-Otaibi, J. S., Mary, Y. S., Mary, Y. S., Trivedi, R., & Chakraborty, B.

Surface enhanced Raman scattering investigation of pioglitazone on silver and silver-gold metal substrates – Experimental analysis and theoretical modeling.

Journal of Molecular Structure, https://doi.org/10.1016/J.MOLSTRUC.2021.130992

Richter, Ł., Paszkowska, K., Cendrowska, U., Olgiati, F., Silva, P., Gasbarri, M., Guven, P., Paczesny, J., & Stellacci, F.
Broad-spectrum nanoparticles against bacteriophage infections.
Nanoscale, https://doi.org/10.1039/D1NR04936D

Aneta Karpińska, Marta Pilz, Joanna Buczkowska, J. Żuk, P., Karolina Kucharska, Gaweł Magiera, Karina Kwapiszewska, & Robert Hołyst
Quantitative analysis of biochemical processes in living cells at a single-molecule level: a case of olaparib–PARP1 (DNA repair protein) interactions.
Analyst, https://doi.org/10.1039/D1AN01769A

Stumpf, B. H., Nowakowski, P., Eggeling, C., Maciołek, A., & Smith, A.-S.
Protein induced lipid demixing in homogeneous membranes.
Physical Review Research, https://doi.org/10.1103/PhysRevResearch.3.L042013

Gizynski, K., Makuch, K., Paczesny, J., Zhang, Y., Maciołek, A., & Holyst, R.
Internal energy in compressible Poiseuille flow.
Physical Review E,  https://doi.org/10.1103/PhysRevE.104.055107

2022

Bielec, K., Kowalski, A., Bubak, G., Witkowska Nery, E., & Hołyst, R.
Ion Complexation Explains Orders of Magnitude Changes in the Equilibrium Constant of Biochemical Reactions in Buffers Crowded by Nonionic Compounds.
The Journal of Physical Chemistry Letters,  https://doi.org/10.1021/ACS.JPCLETT.1C03596

Araki, T., Gomez-Solano, J. R., & Maciołek, A. 
Relaxation to steady states of a binary liquid mixture around an optically heated colloid.
Physical Review E,  https://doi.org/10.1103/PhysRevE.105.014123

Khan, F., Jaoui, M., Rudziński, K., Kwapiszewska, K., Martinez-Romero, A., Gil-Casanova, D., Lewandowski, M., Kleindienst, T. E., Offenberg, J. H., Krug, J. D., Surratt, J. D., & Szmigielski, R.
Cytotoxicity and oxidative stress induced by atmospheric mono-nitrophenols in human lung cells.
Environmental Pollution,  https://doi.org/10.1016/J.ENVPOL.2022.119010

Żuk, P. J., Tużnik, B., Rymarz, T., Kwiatkowski, K., Dudyński, M., Galeazzo, F. C. C., & Krieger Filho, G. C.
OpenFOAM solver for thermal and chemical conversion in porous media.
Computer Physics Communications, https://doi.org/10.1016/J.CPC.2022.108407

Żuk, P. J., Makuch, K., Hołyst, R., & Maciołek, A.  Transient dynamics in the outflow of energy from a system in a nonequilibrium stationary state.
Physical Review E,  https://doi.org/10.1103/PhysRevE.105.054133

Żuk, P. J. 
A brief introduction to contemporary electrokinetics.
Contemporary Physics, https://doi.org/10.1080/00107514.2022.2072565

Karpińska, A., Zgorzelska, A., Kwapiszewska, K., & Hołyst, R.
Entanglement of polymer chains in hypertonic medium enhances the delivery of DNA and other biomacromolecules into cells.
Journal of Colloid and Interface Science, https://doi.org/10.1016/J.JCIS.2022.07.040

Yasmeen, N., Karpinska, A., Kalecki, J., Kutner, W., Kwapiszewska, K., & Sharma, P. S.

Electrochemically Synthesized Polyacrylamide Gel and Core–Shell Nanoparticles for 3D Cell Culture Formation.

ACS Applied Materials & Interfaces, https://doi.org/10.1021/ACSAMI.2C04904

Pacocha, N., Zapotoczna, M., Makuch, K., Boguslawski, J., & Garstecki, P.
You will know by its tail: a method for quantification of heterogeneity of bacterial populations using single-cell MIC profiling.
Lab on a Chip, https://doi.org/10.1039/D2LC00234E

Kowalski, A., Bielec, K., Bubak, G., Żuk, P. J., Czajkowski, M., Sashuk, V., Huck, W. T. S., Antosiewicz, J. M., & Holyst, R.
Effective screening of Coulomb repulsions in water accelerates reactions of like-charged compounds by orders of magnitude.
Nature Communications, https://doi.org/10.1038/s41467-022-34182-z
The reaction speed of like-charged compounds in water is extremely slow due to Coulomb repulsions. Here, the authors boost kinetics up to 5 million times by screening these interactions and increasing the local concentration of reactants using positively charged micelles. They show the effect of two independent systems and present a theoretical explanation.

2023

Karpinska, A., Magiera, G., Kwapiszewska, K., & Hołyst, R.
Cellular Uptake of Bevacizumab in Cervical and Breast Cancer Cells Revealed by Single-Molecule Spectroscopy.
The Journal of Physical Chemistry Letters, https://doi.org/10.1021/ACS.JPCLETT.2C03590

van der Linden, M. N., Everts, J. C., van Roij, R., & van Blaaderen, A.
Realization of the Brazil-nut effect in charged colloids without external driving.
Proceedings of the National Academy of Sciences, https://doi.org/10.1073/PNAS.2213044120
A colloidal Brazil-nut effect was realised using charged colloids. Unlike its' granular counterpart no external shaking is needed to observe this phenomenon.

Ochirbat, E., Zbonikowski, R., Sulicka, A., Bończak, B., Bonarowska, M., Łoś, M., Malinowska, E., Hołyst, R., & Paczesny, J.
Heteroaggregation of virions and microplastics reduces the number of active bacteriophages in aqueous environments.
Journal of Environmental Quality,  https://doi.org/10.1002/JEQ2.20459

Cooperation

  • Krzysztof Burdzy - Department of mathematics University of Washington, USA
  • Patrick Oswald - Ecole Normale Superieure Lyon, France
  • Stefan Diez B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Germany
  • Xizeng Feng - Nankai Univ, Coll Life Sci, State Key Lab Med Chem Biol, Tianjin, China
  • Adam Patkowski, Jacek Gapiński, Stefan Jurga - Faculty of Physics, Adam Mickiewicz University in Poznan, Poland
  • Hans-Jürgen Butt - Max Planck Institute for Polymers, Mainz, Germany
  • Oleg Gang - Brookhaven National Laboratory, USA
  • Douglas Abraham - Oxford University, UK
  • Jerzy Duszyński - Nencki Institute of Experimental Biology, Warsaw, Poland,
  • Teodor Gotszalk - Faculty of Microsystem Electronics and Photonics, Wroclaw University of Technology, Poland
  • Elzbieta Wyroba - Nencki Institute of Experimental Biology, Warsaw, Poland, 
  • Xia Xin - Shandong Univ, Natl Engn Technol Res Ctr Colloidal Mat, Jinan, China 
  • Hongguang Li - Chinese Acad Sci, Lanzhou Inst Chem Phys, Lab Clean Energy Chem & Mat, Lanzhou, China
  • Remigiusz Worch - Institute of Physics, Polish Academy of Sciences, Warsaw, Poland

Financing

Current funding

  • Polish National Agency for Academic Exchange (NAWA), grant no. PPN/ULM/2019/1/00257, "Diffusion and flow in interacting complex fluids",  2020-2022, leader Jeffrey Everts, PhD.
  • OPUS 17 Project No. UMO-2019/33/B/ST4/00557 “Changes of intracellular transport during cell death”, leader Karina Kwapiszewska, PhD Eng., 2019-2022
  • NCBR project Lider 0033/L-9/2017 "Method for quantification of internalization of chemical and biological molecules into living cells", leader Karina Kwapiszewska, PhD Eng., 2019 - 2022
  • NCN project Maestro 2016/22/A/ST4/00017 "New method for determination of equilibrium constant for complex formation, concentrations and diffusion coefficients in solutions and living cells at nanomolar down to picomolar concentration of reagents", leader Professor Robert Hołyst, 2017 - 2021
    • 1 Nov 2017  Marta Pilz and Patrycja Kuźma (PhD students) joined project.
    • 1 Oct 2017  Wiktoria Karwicka (MsC student) started participation in project.
    • 1 Jul 2017  Grzegorz Bubak (Postdoc) and Krzysztof Bielec (PhD student) joined project.
    • 20 Jun 2017  Arrival of new laserlines for confocal microscope system from PicoQuant.
    • 15 Jun 2017  Final deadline for submitting applications for PhD position at MAESTRO 8 grant.

Previous funding

Leader Professor Robert Hołyst

  • NCN project SYMFONIA 2013/08/W/NZ1/00687 „Towards quantitative biology via novel method of mobility measurement in the intracellular compartment: interactions of proteins with intracellular structures of glycogen and mitochondria” (leader Professor Jerzy Duszyński from the Nencki Institute of Experimental Biology, partner Professor Robert Hołyst) 2014 - 2018
  • NCN project OPUS 2014/13/B/ST3/04414 „Influence of the mean free path in vapor, temperature, pressure and vapor composition on evaporation at the nano and microscale” (leader Daniel Jakubczyk, Ph.D., D.Sc., Eng. from Institute of Physics, partner Professor Robert Hołyst) 2015 - 2018
  • NCN project Opus 2012/07/B/ST4/01400 „Taylor Dispersion Analysis in coiled capillaries at high flow rates – new tool in analytical chemistry for determination of equilibrium constant for ligand - macromolecule binding” 2013-2016
  • NCBIR project PBS “Commercial method for production of SERS substrates for fast and sensitive biomedical sensors” 2013-2015 applied research
  • NCN project Maestro 2011/02/A/ST3/00143 “Length-scale dependent nano-viscosity in soft matter systems and in living cells” 2012-2016
  • Noblesse project EU NanOtechnology, Biomaterials and aLternative Energy Source for ERA integration FP7-REGPOT-CT-2011-285949-NOBLESSE, 2011-2014
  • Patent Plus 52/PMPP/U/7‑03.10/E-64/2100
  • European Science Foundation and Ministry of Science and Higher Education “Physical phenomena in small systems: evaporation at the nano and microscale” 2010-2013
  • EFS 750/N-ESF-EPSD/2010/0 "Exploring the physics of small devices" 2010-2013
  • Foundation for Polish Science project TEAM/2008-2/2 “From nano to macroscale: motion of proteins, protein charge ladders and nanoparticles in complex liquids” 2009-2013 PI EU and structural funds
  • Project POIG.01.01.02-00-008/08 „Quantum semiconductor nanostructures for medicine and biological applications - development and commercialization of new generation of appartus for molecular diagnostics” 2008-2013
  • Foundation for Polish Science project Mistrz Nr 3/2007 “Physics inspired by nanotechnology and biology” 2007-2010
  • EFS/MNiSW SONS 2 "Complexity Across Lenghtscales in Soft Matter (SCALES)" 2007-2010
  • MNiSW project N202 002 32/0090: “Nanotechnology inspired physics: evaporation and condensation at the nanoscale” 2007-2009
  • KBN project 1PO3B 073 30 „Physics inspired by biology: motion of nanoobjects in complex liquids” 2006-2008
  • ESF and MNiSW project EFS/21/2006 “Self-organization of colloids in liquid crystals and block copolymers” 2006-2009
  • KBN projec 1PO3B06530 „Space distribution in reaction diffusion system” 2006-2007
  • KBN project 2P03B00923 „Kinetics and dynamics of phase transitions: experiment and simulations” 2002-2005

Other members of the group

  • NCN project Sonata Bis 2017/26/E/ST4/00041 "Modulation of Stability of Virions – a Fight for and Against Viruses", leader Jan Paczesny, PhD, 2018 - 2022
  • NCN project HARMONIA 2015/18/M/ST3/00403 "Active Brownian motion of functional microparticles in complex fluids in the bulk and under spatial confinement", leader DSc. Anna Maciołek, 2016 - 2019
  • NCN project Preludium 2017/27/N/ST4/0235 "Development of fast and efficient deposition of analyte in the electric field for improvement of sensing and biosensing", leader MSc. Eng. Łukasz Richter, 2018 - 2019
  • NCN project Sonata 2012/07/D/ST4/02183 "Ilościowa analiza procesu cięcia DNA enzymami restrykcyjnymi w zatłoczonym środowisku za pomocą spektroskopii korelacji fluorescencji", leader Sen Hou, 2013-2016
  • NCN project Sonata 2012/07/D/ST5/02240 „Opracowanie szybkiego i czułego sensora do detekcji bakterii opartego o receptory bakteriofagowe”, leader Jan Paczesny, 2013-2016
  • MNiSW project Iuventus Plus IP2012 015372 "Analysis of the viscosity of bacterial lysates at the nano- and macroscopiclength-scale", leader Tomasz Kalwarczyk, 2013-2015
  • MNiSW project Iuventus Plus IP2012 046572 "Thin films of ZnO quantum dots", leader Jan Paczesny, 2012-2015
  • MNiSW project Iuventus Plus IP2011 021771 "Studies of the activation energy for diffusion of proteins in aqueous so-lutions of polyethylene glycol", leader Tomasz Kalwarczyk, 2012-2013
  • MNiSW project Iuventus Plus IP2010 028270, "Badanie zjawiska odwracalnosci w warstwach Langmuira utworzonych na granicy faz woda-powietrze z czasteczek bolaamfifilowych ciekłych kryształów oraz innych amfifilowych zwiazków", leader Patrycja Nitoń, 2010-2011
  • Foundation for Polish Science projecrt POMOST_C/43, leader Patrycja Nitoń, 2010-2011
  • Preludium 2011/01/N/ST3/00865 “Analysis of the viscosity of protein solutions at the nano- and macro-scopic length-scale”, leader Tomasz Kalwarczyk, 2011-2013
  • Preludium 2011/01/N/ST5/02917 "Self-assembly of bolaamphiphiles", leader Jan Paczesny, 2011-2012
  • Diamentowy grant MNiSW (konkurs adresowany do studentów prowadzących badania naukowe na uczelniach lub w instytutach) otrzymali studenci: Piotr Trochimczyk ("Obserwacja agregacji DNA za pomocą spektroskopii korelacji fluorescencji oraz mikroskopii sił atomowych", 2015) i Krzysztof Sozański, ("Makro- i nanolepkość w roztworach polimerów: przejście od wysokich do niskich stężeń", 2012)
  • Foundation for Polish Science projecrt Inter 74/UD/SKILLS/2014 "Bakterie, które oszukują test Grama – szybka adaptacja do stresu mechanicznego" leader Jan Paczesny, 2014-2015
  • KBN 1P03B09230 "Eksperymentalne badania przejść fazowych w dwuwymiarowych układach uporządkowanych"  Andrzej Żywociński, 2006-2009

See also