Faculty of Physics University of Warsaw > Events > Seminars > Soft Matter and Complex Systems Seminar

Soft Matter and Complex Systems Seminar

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room 1.40, Pasteura 5 at 09:30

Bartosz Różycki (IF PAN)

Conformational ensemble of the full-length nucleocapsid protein of SARS-CoV-2: coarse-grained simulations and SAXS experiments

The nucleocapsid protein of the SARS-CoV-2 virus comprises two RNA-binding domains and three regions that are intrinsically disordered. While the structures of the RNA-binding domains have been solved using protein crystallography and NMR, current knowledge of the conformations of the full-length nucleocapsid protein is rather limited. To fill in this knowledge gap, we combined coarse-grained molecular simulations with data from small-angle X-ray scattering (SAXS) experiments using the ensemble refinement of SAXS (EROS) method. Our results show that the dimer of the full-length nucleocapsid protein exhibits large conformational fluctuations with its radius of gyration ranging from about 4 to 8 nm. The RNA-binding domains do not make direct contacts. The disordered region that links these two domains comprises a hydrophobic alpha-helix which makes frequent and nonspecific contacts with the RNA-binding domains. Each of the intrinsically disordered regions adopts conformations that are locally compact, yet on average, much more extended than Gaussian chains of equivalent lengths. We offer a detailed picture of the conformational ensemble of the nucleocapsid protein dimer under near-physiological conditions, which will be important for understanding the nucleocapsid assembly process.

room 1.40, Pasteura 5 at 09:30

Piotr Śmieja, Hanifah Darmawanti, Maks Walewski (IFT UW)

Soft matter student talks

On Friday 3 June 2022 at 9:30 AM we are hosting short presentations by:

Piotr Śmieja
Analysis of the solution dolines in the southwestern Slovenia

Solution dolines are a predominant feature of the limestone karst plateaus in southwestern Slovenia. Their origin is attributed to the reactive-infiltration instability in the carbonate rock dissolution. They are an interesting object of study not only from the geographical but also physical point of view. I will present a short summary of my analysis of their shapes and spatial distribution including methods used and obtained results.

Hanifah Darmawanti
Analysis of renaissance ceramics body and pigments by non-invasive X-Rays Fluorescence technique

The research aims to investigate and analyse the characteristics of ceramics' bodies and the composition of pigments on their decorations. By using fluorescent X-Rays spectroscopy (XRF) technique, the assessment of materials, ages, and elements present even in trace amounts in art pieces help us to understand the artists' method of creating them and also to maintain those art pieces. This analysis uses the characteristic low energy X-Rays to identify the elemental composition of the objects' surface.

Maks Walewski
What ultracold physics can teach us about life?

Cooling atomic, ionic and molecular systems down to ultracold temperatures offer insight into a wide set of otherwise unobservable quantum phenomena. I am going to describe the reasons behind it and show how they can help us understand the preference for the molecules of one handedness over the other, manifest in the biological systems.

room 1.40, Pasteura 5 at 09:30

Yves Pomeau (LadHyX, Ecole Polytechnique)

Statistical physics and the "interpretation" of quantum mechanics

The equation of quantum mechanics (Schrodinger and Dirac) are formally deterministic, that seems to forbid to introduce a fundamental uncertainty in the predictions one can make from given initial data, a difficulty in the logic present from the very beginnings of quantum mechanics. I shall explain how to deal with this question by returning to the original paper by Dirac on the emission of photons by an atom in an excited state. This is illustrated by a detailed discussion of the dynamics of a two-level atomic state pumped by a resonant classical field, something representing experimental situations.

room 1.40, Pasteura 5 at 09:30

Antoine Sellier (LadHyX, Ecole Polytechnique)

MHD viscous flow about a translating slip sphere

The MHD viscous flow about a slip solid insulating sphere translating in a conducting Newtonian liquid parallel with an imposed uniform and steady magnetic fields is considered. The adopted slip condition on the sphere is the usual Navier condition with a prescribed slip length possibly varying in the direction of the sphere translation. A theoretical formulation valid for such an arbitrary slip distribution and providing both the flow about the sphere and the drag it experiences is proposed. An efficient numerical implementation is then performed for two illustrating examples: a uniform slip length and a slip length with constant slope. The resulting drag force sensitivity to the Hartmann number and the slip magnitude and distribution will be thereby reported and discussed for those examples.

room 1.40, Pasteura 5 at 09:30

Marta Wacławczyk (IGF FUW)

Detecting non-equilibrium states in atmosheric turbulence

Atmospheric turbulence is a complex phenomenon, characterized by the presence of a plethora of scales (eddies) ranging from small viscosity-dominated to large energy-containing structures. Turbulence may undergo large space and time variations due to rapidly changing external conditions, it may be locally suppressed or enhanced. In this presentation we address non-equlibrium states where, because of non-stationarity, turbulence deviates from the classical Kolmogorov's picture. Such states can be described by different, non-classical scaling relations, which, however, appear to be universal. Based on these theoretical analyses we show that it is possible to retrieve information on temporal tendencies in a given flow. We focus on the stratocumulus-topped boundary layers and investigate data available from field measurements performed by research aircrafts.

room 1.40, Pasteura 5 at 09:30

Panagiotis Theodorakis (IF PAN)

Pinning and its role in the directed motion of fluids

Pinning of liquid droplets on solid substrates is ubiquitous and plays an essential role in many applications, especially in various areas such as microfluidics and biology. In some cases, this phenomenon can offer new possibilities for technological exploitation, while in other cases it can pose challenges. In this talk, I will discuss the details of pinning and depinning processes in the case of liquid droplets on solid substrates and possible ways of exploitation. Then, I will present our results and analysis on the rugotaxis phenomenon, that is, the spontaneous motion of a fluid onto wavy substrates with gradient in the wavelength, and discuss the role of pinning. Our analysis is based on molecular dynamics simulations of a coarse-grained model.

room 1.40, Pasteura 5 at 09:30

Paweł Zin (NCBJ – National Centre for Nuclear Research)

Non-existence of causal classical electrodynamics of point scalar charged particles

Usually at last pages of classical electrodynamics books it is shown, that due to radiation emitted by accelerating point charged particles, Lorentz force is not enough to provide energy and momentum conservation in the system. The need of additional force appears. The most popular form of this force (known as self-force or radiation reaction force) is the Lorentz-Abraham-Dirac (LAD) force proportional to time derivative of acceleration. However LAD force is known to provide non-causal particle trajectories (the particle starts to move before the arrival of the external electromagnetic field). To cure this behavior few causal theories were proposed. However they all lead to unphysical phenomena. The long search for correct theory suggests that such does not exist. In my talk I will present a proof of non-existence of causal classical electrodynamics of point scalar charged particles.

room 1.40, Pasteura 5 at 09:30

Grzegorz Łach (IFT UW)

Residual entropy of water ice

Water is known to form ~20 different solid phases. In many of them, the orientations of water molecules in the crystal lattice are disordered - the crystal itself is one of a macroscopic number of allowed configurations. This leads to residual entropy, seemingly violating the 3rd law of thermodynamics. Half a century ago, configurational entropy was calculated exactly for 2D ice model on a square lattice (Lieb, 1967). For other lattices, both 2D and 3D, not only the analytic values of the residual entropies are not known, but also their numerical estimates are surprisingly inaccurate. For 3D ice models on hexagonal (ice-Ih) and cubic (ice-Ic) lattices, their residual entropies have been estimated by Pauling (1932) and improved by Nagle and Onsager (1966) but since then there was no noticeable improvement neither in analytic results nor numerical calculations. This left some unresolved questions, which I will address during the talk.

join us at 09:30

Endre Joachim Mossige (Norwegian University of Life Sciences NMBU, Norway)

Balloon drops and other shapes with miscible kitchen fluids

The kitchen is a hub of fluid mechanics where drops play a prominent role: the coffee ring effect, the transition from jetting to dripping in a tap, and the mesmerizing display of soap films during dish washing are everyday examples. These flows concern immiscible fluids and are well studied due to their omnipresence in technical situations such as inkjet printing and microfluidic encapsulation; however, transport problems involving miscible fluids have enjoyed far less attention, which is surprising given their rich dynamics. A canonical mixing problem from the kitchen concerns the sweetening of tea with honey, and we have previously shown (Walls et al., JFM, 2018) that sessile drops form miscible “skirts” due to free convection, and we report a remarkable jetting phenomenon for pendant drops. In this talk, we invert the fluids and look at freely suspended water drops rising through more dense, more viscous miscible liquids (Mossige et al., Phys. Fluids, 2021). We track the shape of these balloon shaped drops, as well as their velocities and volumes, and use a simple scaling relation to rationalize our findings. Our experiments make use of edible ingredients such as water, corn syrup and food coloring, and can be performed at home with simple kitchen tools and a cell phone camera. These types of kitchen flow experiments are vehicles for accessible and affordable science education and are hotspots for curiosity-driven research (Mathijssen, Lisicki, Prakash, Mossige, arxiv.org/abs/2201.12128, 2022).

The seminar will be held on Zoom
https://us02web.zoom.us/j/82784273907

join us at 09:30

Mateusz Denys (IF PAN)

How surfactants affect cloud droplet activation?

Atmospheric aerosols usually consist of inorganic salts and organic substances, where a significant part is surfactants, that is, amphiphilic molecules containing a hydrophilic and a hydrophobic part. Due to their amphiphilic character, surfactants preferentially adsorb at the surface of liquids lowering the surface tension of the interfaces, thus affecting processes, such as droplet coalescence, development of precipitation and (ultimately) cloud lifetime.

We created a numerical model of cloud droplet formation with a presence of surfactant and salt. The model is based on the Lagrangian particle-based microphysics scheme Super-Droplet Method (SDM). By means of the SDM, we provided an evidence that surfactants influence cloud formation.

The seminar will be held on Zoom
https://us02web.zoom.us/j/82784273907

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