Soft matter is a collective term for complex fluids such as polymers, colloids, surfactants or liquid crystals. Soft matter is typically flexible, easily deformed, sensitive to external field, and often too soft to be solid, yet too hard to be liquid. Such matter is omnipresent in nature in form of tissues, membranes, coacervate droplets, peptides or cell nuclei. Rubber, hydrogels, isolation foams, micellar water, mayonnaise, yogurts or wall paint are just a few among derived soft matter products, that we use on a daily basis.
I wish to understand relation between microscopic structure and resultant macroscopic properties of different classes of soft matter, focusing mainly on polymers. This includes investigation of phase transitions, clustering, self-organization, dynamics and how to regulate and control these phenomena.
My main tools are Molecular dynamics and Monte Carlo simulations akin to virtual experiments, in which one mimics a fictitious dynamics of molecules in complex environments. Simulations enable to test theoretical models by solving them numerically, and they can be also used to mirror and interpret or predict experimental results. Computer simulations have proven to be a strong tool, bridging both physics of the microscopic world with the macroscopic one, and also experiments with theories.
I use a range of computational methods allowing to capture phenomena across many length scales, from the atomic one via Molecular dynamics, through nano- and mesoscale via Multi-particle collision dynamics up to macroscopic scale via continuous models derived from Density functional theory.
#rings #knots #linking #threading #twisting #entanglement #catenanes #kinetoplasts #topology #fractals
Even such a simple operation as connecting two ends of a linear polymer strand, thereby turning it into a ring, can have drastic impact on its properties. In contrast to the open-ended linear architecture, ring topology allows (i) linking several rings into chains, (ii) threading of the ring by other object like an eye of a needle, (iii) or tying permanent molecular knots. It is not a coincidence, that biomacromolecules such as plasmids DNA or mitochondrial DNA are ring-shaped, as this unique topology brings about extraordinary means of their bioregulation.
❓ How does the ring topology of polymer affect its properties? Are the ring polymers fluid-like or solid-like? How do they behave in flows? Do they form glasses?
❓ How do the rings respond to internal stimuli and fields? Can we open or close the interior of the ring by change of pH or temperature? Can we harvest this in smart materials?
Staňo et al.: Mixing linear polymers with rings and catenanes: bulk and interfacial behavior. 2023, Macromolecules, 56(20)
Staňo et al.: To thread or not to thread? Effective potentials and threading interactions between asymmetric ring polymers. 2023, Soft Matter, 19(1)
#polyelectrolytes #coacervates #condensates #polypeptides #gels #patchycolloids #chargeregulation #proteins
Most of the building blocks of nature are highly charged macromolecules - DNA, RNA, many polypeptides or hyaluronic acid. Of the most important actors in the above systems is non-covalent Coulomb interaction between the charged groups, which provide the driving force for compaction of viral genome, DNA-histone condensation, assembly of actin bundles or formation of membraneless organelles and complex coacervates, all of which can be reversibly regulated by change of pH or salt conditions. Many conventional polyelectrolytes are water-soluble and bio-compatible, making them perspective candidates for medical applications, such as drug delivery or biomarker sensing.
❓ Under what conditions do the charged macromolecules undergo phase transitions? Can we harvest the charge regulation in design of responsive materials?
❓ Can we use multiphase systems of polyelectrolytes, such as hydrogels or polyelectrolyte complexes for sequestration of solutes between the phases? How efficient are such materials for wastewater treatment or drug delivery?
Staňo et al.: Sequestration of small ions, weak acids and bases by polyelectrolyte complex studied by simulation and experiment. 2024, Macromolecules, 57(3)
Staňo et al.: Electrostatically Cross-Linked Reversible Gels—Effects of pH and Ionic Strength. 2021, Macromolecules, 54(10)
Staňo et al.: Multivalent counterions accumulate in star-like polyelectrolytes and collapse the polymer in spite of increasing its ionization. 2020, Soft Matter, 16(10)
#dnaorganization #topoisomerase #supercoiling #plasmids #dnananotechnology #writhing #dnaminirings
Understanding organization of DNA inside and outside of the cell nuclei poses one of the most active open problems in biophysics. While the principles of base-pairing and sequence-specific design is well established in both living matter and DNA nanotechnology, geometrical and topological aspects of DNA polymer strands are still poorly understood. How do the topological constraints affect the structure of DNA and how is the structure regulated by enzymes such as topoisomerases or gyrases?
❓ What is the shape and size of DNA rings in solutions and in melts? Under what conditions do they self-assemble or cluster?
❓ How can we regulate twist and writhe of DNA molecules? How does supercoiling affect the properties of DNA materials?
Staňo et al.: Cluster Formation in Solutions of Polyelectrolyte Rings. 2023, ACS Nano, 17(21)
Polyelectrolytes, Coacervates, Charge Regulation:
Peter Košovan & Sebastian P. Pineda (Charles University in Prague)
Saskia Lindhoud & Jéré J. van Lente (University of Twente)
Christian Holm & David Beyer (University of Stuttgart)
Pablo M. Blanco (Norwegian University of Science and Technology)
Ring Polymers & Topology of DNA
Christos N. Likos & Ján Smrek & Vittoria Sposini (University of Vienna)
Davide Michieletto & Filippo Conforto (University of Ediburgh)
Sergei A. Egorov (University of Virginia)
Emmanuel Stiakakis (Forschungszentrum Jülich)