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 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)
2.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)
3.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.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