Magdalena Gruziel-Słomka, Ph.D.

Department of Biosystems and Soft Matter (ZBiMM)
Division of Complex Fluids (PFPZ)
position: specialist
telephone: (+48) 22 826 12 81 ext.: 421
room: 322
e-mail: mgruziel

Doctoral thesis
2008-06-16Badanie energii swobodnej solwatacji modelowych układów molekularnych z wykorzystaniem metod fizyki statystycznej i obliczeniowych  
supervisor -- Prof. Bogdan Lesyng, Ph.D., Dr. Habil., UW
1343 
Recent publications
1.Gruziel-Słomka M., Kondratiuk P., Szymczak P., Ekiel-Jeżewska M.L., Stokesian dynamics of sedimenting elastic rings, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/c9sm00598f, Vol.15, pp.7262-7274, 2019
Abstract:

We consider elastic microfilaments which form closed loops. We investigate how the loops change shape and orientation while settling under gravity in a viscous fluid. Loops are circular at the equilibrium. Their dynamics are investigated numerically based on the Stokes equations for the fluid motion and the bead–spring model of the microfilament. The Rotne–Prager approximation for the bead mobility is used. We demonstrate that the relevant dimensionless parameter is the ratio of the bending resistance of the filament to the gravitation force corrected for buoyancy. The inverse of this ratio, called the elasto-gravitation number [scr B, script letter B], is widely used in the literature for sedimenting elastic linear filaments. We assume that [scr B, script letter B] is of the order of 104–106, which corresponds to easily deformable loops. We find out that initially tilted circles evolve towards different sedimentation modes, depending on [scr B, script letter B]. Very stiff or stiff rings attain almost planar, oval shapes, which are vertical or tilted, respectively. More flexible loops deform significantly and converge towards one of several characteristic periodic motions. These sedimentation modes are also detected when starting from various shapes, and for different loop lengths. In general, multi-stability is observed: an elastic ring converges to one of several sedimentation modes, depending on the initial conditions. This effect is pronounced for very elastic loops. The surprising diversity of long-lasting periodic motions and shapes of elastic rings found in this work gives a new perspective for the dynamics of more complex deformable objects at micrometer and nanometer scales, sedimenting under gravity or rotating in a centrifuge, such as red blood cells, ring polymers or circular DNA.

Affiliations:
Gruziel-Słomka M.-IPPT PAN
Kondratiuk P.-University of Warsaw (PL)
Szymczak P.-University of Warsaw (PL)
Ekiel-Jeżewska M.L.-IPPT PAN
2.Gruziel M., Thyagarajan K., Dietler G., Stasiak A., Ekiel-Jeżewska M.L., Szymczak P., Periodic Motion of Sedimenting Flexible Knots, PHYSICAL REVIEW LETTERS, ISSN: 0031-9007, DOI: 10.1103/PhysRevLett.121.127801, Vol.121, No.12, pp.127801-1-6, 2018
Abstract:

We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwined loops, oscillating periodically around each other. We then recover this motion numerically and find out that it is accompanied by a very slow rotation around the vertical symmetry axis. We analyze the dependence of the characteristic timescales on the chain flexibility and aspect ratio. It is observed in the experiments that this oscillating mode of the dynamics can spontaneously form even when starting from a qualitatively different initial configuration. In numerical simulations, the oscillating modes are usually present as transients or final stages of the evolution, depending on chain aspect ratio and flexibility, and the number of loops.

Affiliations:
Gruziel M.-IPPT PAN
Thyagarajan K.-École Polytechnique Federale de Lausanne (CH)
Dietler G.-École Polytechnique Federale de Lausanne (CH)
Stasiak A.-École Polytechnique Federale de Lausanne (CH)
Ekiel-Jeżewska M.L.-IPPT PAN
Szymczak P.-University of Warsaw (PL)
3.Gruziel M., Szymczak P., From ribbons to tubules: a computational study of the polymorphism in aggregation of helical filaments, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/c5sm00652j, Vol.11, pp.6294-6304, 2015
Abstract:

A simple, coarse-grained model of chiral, helical filaments is used to study the polymorphism of fibrous aggregates. Three generic morphologies of the aggregates are observed: ribbons, in which the filaments are joined side-by-side, twisted, helicoidal fibrils, in which filaments entwine along each other and tubular forms, with filaments wound together around a hollow core of the tube. A relative simplicity of the model allows us to supplement numerical simulations with an analytic description of the elastic properties of the aggregates. The model is capable of predicting geometric and structural characteristics of the composite structures, as well as their relative stabilities. We also investigate in detail the transitions between different morphologies of the aggregates.

Affiliations:
Gruziel M.-other affiliation
Szymczak P.-University of Warsaw (PL)
4.Gruziel M., Dzwolak W., Szymczak P., Chirality inversions in self-assembly of fibrillar superstructures: a computational study, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/c3sm27961h, Vol.9, pp.8005-8013, 2013
Abstract:

The formation of aggregates of helical fibrils is analyzed numerically. The aggregate morphology, chirality and stability are studied as a function of temperature and helical pitch of individual fibrils. The simulations show the existence of a critical pitch above which the handedness of the aggregates is opposite to that of the constituting fibrils. We also observe and analyze the process of spontaneous chirality inversion of individual fibrils within the aggregates. This inversion is accompanied by a helical wave propagating along the fibril axis, with a kink separating left-handed and right-handed regions moving along the fibril. The frequency of this process is strongly dependent on the initial pitch of the fibrils with a local maximum near the critical pitch.

Affiliations:
Gruziel M.-other affiliation
Dzwolak W.-University of Warsaw (PL)
Szymczak P.-University of Warsaw (PL)

Conference abstracts
1.Szymczak P., Gruziel-Słomka M., Kondratiuk P., Ekiel-Jeżewska M.L., Sedimentation of elastic loops in a viscous fluid, Bulletin of the American Physical Society, ISSN: 0003-0503, Vol.63, No.13, pp.368, 2018
2.Gruziel M., Thyagarajan K., Dietler G., Szymczak P., Ekiel-Jeżewska M.L., Dynamics of knotted flexible loops settling under a constant force in a viscous fluid, Bulletin of the American Physical Society, ISSN: 0003-0503, Vol.62, No.14, pp.81, 2017