Poster Presentations

Co-authors: Cheng Tan (RIKEN Center for Computational Science Kobe), Zuzanna Staszałek (Institute of Physics, Polish Academy of Sciences), Maja K. Cieplak-Rotowska (Institute of Physics, Polish Academy of Sciences, and University of Warsaw), Marc R. Fabian (McGill University), Nahum Sonenberg (McGill University), Michał Dadlez (Institute of Biochemistry and Biophysics, Polish Academy of Sciences), Yuji Sugita (RIKEN Center for Computational Science Kobe), Anna Niedźwiecka (Institute of Physics, Polish Academy of Sciences)

Abstract: GW182 is a fuzzy, intrinsically disordered scaffold protein that binds the CNOT1 subunit of the CCR4–NOT deadenylase complex, driving microRNA-mediated post-transcriptional gene silencing¹. CCR4–NOT also participates in a distinct silencing pathway directed by the intrinsically disordered protein tristetraprolin (TTP)². While the CNOT1 residues mediating TTP binding have been characterised³, the molecular mechanism by which CNOT1 recognises GW182 remains elusive.

Here, we integrate fluorescence correlation spectroscopy (FCS) with liquid–liquid phase separation (LLPS) assays to elucidate the basis of CNOT1 recognition of GW182. We show that the GW182 silencing domain (SD) undergoes LLPS with LCST-type behaviour driven by a tryptophan-dependent mechanism and forms two-component condensates with CNOT1, consistent with a host–client interaction⁴ that is perturbed by single-point mutations. To quantify diffusion kinetics of proteins and their complexes under local crowding within condensates, we couple FRAP (fluorescence recovery after photobleaching) with FRET (Förster resonance energy transfer). This tandem FRET–FRAP approach discriminates specifically interacting proteins from those passively retained by crowding and, leveraging FRET’s angstrom-scale distance sensitivity, offers a general, highly selective strategy for identifying specific protein complexes in crowded environments.

Acknowledgments: This work was supported by the NCN grants no. UMO-2016/22/E/NZ1/00656 to A. N. and no. UMO-2023/49/B/NZ1/04320 to M. K. B. The studies were performed in the NanoFun laboratories co-financed by ERDF within the POIG.02.02.00-00-025/09 project.

Co-authors: Anna Krztoń-Maziopa (Warsaw University of Technology)

Abstract: Iron chalcogenides represent a vast group of materials that display a wide range of crystal structure and morphology,  as well as different physical and chemical properties. Among those materials, the tetragonal phase of non-stoichiometric iron selenide (β-FeSe1-x) is of particular interest, due to its layered structure and substantial van der Waals gaps (~2,8 Å), which makes it capable of accommodating foreign species in this matrix. This is particularly significant in the domain of electrochemical energy generation and storage, as well as in the development of superconductors and magnetic materials through precise manipulation of band structure by means of structural and electronic tuning, resulting from intercalation and doping. So far there have been scientific reports about intercalation of β-FeSe1-x with various species including alkali metal ions, Lewis base adducts or organic ammonium ions[1][2]. Potential applications of intercalated β-FeSe1-x include new materials for energy production and conversion, potential catalysts and absorbers in dye-sensitised solar cells [3] or electrode material in lithium-sulphur batteries [4]. 

The preparation of these functional materials primarily involves the use of chemical intercalation. However, due to the strong reducing enviroment during the intercalation reaction, the host material itself may undergo decomposition, resulting in the formation of undesirable phases and alterations to the material's properties. In order to overcome these obstacles, a novel method of electrochemical intercalation of β-FeSe1-x is being developed. So far, the synthesis of intercalants with tetramethylammonium (TMA+) and cetyltrimethylammonium (CTA+) ions has been achieved through electrointercalation methods [2][5]. In this work,  the morphology and crystal structure of different β-FeSe 1-x intercalates will be discussed, along with potential modifications to the β-FeSe 1-x host matrix, with a focus on potential application of layered iron chalcogenides in the domain of electrochemical energy generation.

Acknowledgments:

Co-authors: Pham Dinh Quoc Huy (Institute of Physics, Polish Academy of Sciences), Michał Wojciechowski (Institute of Physics, Polish Academy of Sciences)

Abstract: We present a novel computational approach for investigating interactions between intrinsically disordered regions (IDRs) that contribute to protein aggregation. The method begins with the generation of starting complex structures using the HADDOCK web server, which incorporates biochemical and biophysical data to guide docking. These initial models are then subjected to all-atom molecular dynamics simulations in explicit solvent to explore the conformational landscape and refine the interaction interfaces. To assess the reliability and consistency of the observed interactions, we employ a contact map overlap analysis, enabling detailed comparison of interaction patterns across simulation trajectories. As a case study, we apply this methodology to the well-characterized transactivation domain (TAD) of the tumor suppressor p53 and its interaction with MDM2 (Murine Double Minute 2), its principal negative regulator. Both proteins contain significant intrinsically disordered regions, and their interaction forms a critical node in pathways regulating cell cycle progression and apoptosis. This approach provides a versatile framework for studying IDR-mediated protein-protein interactions.

Acknowledgments: We gratefully acknowledge Polish high-performance computing infrastructure PLGrid (HPC Center: ACK Cyfronet AGH) for providing computer facilities and support within computational grant no. PLG/2024/017274

Co-authors: 

Abstract: During the flow of a matrix-dissolving fluid through porous media, positive feedback between flow and reaction can create various, time-evolving forms. These forms exhibit a range of geometries, from complex, cave-like structures (wormholes) to simple frontal dissolution. This complex example of hydrodynamic instability is sensitive not only to flow parameters but also to the spatial properties of the porous media. While the effects of flow rate and reaction rate on the morphologies of wormholes are now understood, the mechanisms governing their propagation dynamics remain significantly less characterized. 

This study focuses on the fast-progressing dominant wormhole regime, which is relevant in a range of industrial and natural cases, including carbon capture and storage (CCS). To understand the dynamics of fluid interaction with the surrounding porous matrix, high temporal and spatial resolution data are required. We report on a series of experiments that aimed to capture 4D X-ray computed tomography (X-CT) high-resolution images of developing wormholes under different flow conditions. Such datasets allowed for the evaluation of a wide range of geometrical properties, which could be correlated with both numerical and analytical studies. In this communication, we particularly focus on how the dynamics of the instability that grows in natural, highly heterogeneous rock relate to an often-used analytical model of a tube growth and the onset of the instability. 

Acknowledgments: NCN CEUS UNISONO 2020/02/Y/ST3/00121, ID-19 beamline at the European Synchrotron Radiation Facility (ESRF), Computational resources from ICM UW

Co-authors: Anna Krztoń- Maziopa (Warsaw University of Technology)

Abstract: The search for two-dimensional (2D) layered materials beyond graphene remains one of the central challenges in modern materials science. Honeycomb-type atomic lattices are of particular interest due to their unique physicochemical properties and potential in energy-related applications. In this work, we present an electrochemical strategy for the synthesis of layered Zintl-phase materials, consisting of ZnSb sheets with sp² hybridization and honeycomb ordering, obtained via controlled intercalation and cation exchange of polycrystalline zinc antimonide hosts. Electrochemical incorporation of metal ions enables systematic tuning of the structure and electrical properties, providing a versatile pathway for tailoring composition and performance. The obtained materials were characterized using X-ray diffraction (XRD) to resolve their crystal structure, while scanning electron microscopy (SEM) coupled with energy-dispersive X-ray spectroscopy (EDX) was employed to examine morphology and chemical composition. Correlation of these structural and compositional features with electrical measurements revealed direct structure–property relationships, underscoring the role of electrochemical engineering in controlling the functionality of layered ZnSb phases. 

Acknowledgments:

Co-authors: Agnieszka Michaś (Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences), Tomasz Wojciechowski (International Research Centre MagTop, Institute of Physics, Polish Academy of Sciences), Anna Niedźwiecka (Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences)

Abstract: Non-classical crystallization theory challenges traditional models by proposing that crystal formation proceeds through intermediate states such as amorphous calcium carbonate (ACC) or polymer-induced liquid precursors (PILPs) [1]. Although ACC has been identified in the coral Stylophora pistillata [2], direct evidence for PILPs remains limited, with most insights inferred from the analysis of solid phases. In the context of biomineralization in living organisms such as corals, the polymers that are thought to be involved in skeleton formation are coral acid-rich proteins (CARPs) [3], which are secreted at the coral tissue–skeleton interface. These proteins have been shown to bind calcium and influence crystal morphology [3] and polymorph selection [4].

In this study, we demonstrate that the aspartic- and glutamic acid-rich protein (AGARP), an intrinsically disordered protein with an exceptionally high charge of -148 e per molecule and the first cloned CARP from the model coral species, Acropora millepora, modulates calcium carbonate formation via liquid-liquid phase separation (LLPS) [5].

Using fluorescence correlation spectroscopy, we observed that AGARP and Ca²⁺ ions form early aggregates in non-crowded, water-like solutions prior to the emergence of ACC, as confirmed by scanning electron microscopy with energy-dispersive X-ray spectroscopy.

On the other hand, under molecular crowding conditions that mimic the endoplasmic reticulum and extracellular matrix environments, where AGARP is processed after biosynthesis and exported, respectively, AGARP forms liquid protein–calcium condensates (LPCCs) through LLPS, as revealed by confocal laser scanning fluorescence microscopy and fluorescence recovery after photobleaching experiments. When exposed to carbonate ions, these LPCCs serve as crystallization precursors, and the resulting CaCO3 phases exhibit smooth edges that differ markedly from the sharp edges formed in the absence of AGARP.

Our findings suggest that the LPCCs could be biologically relevant precursors in calcium carbonate biomineralization and highlight the importance of LLPS and macromolecular crowding in this process. This study provides a new perspective on the processes involved in the skeleton formation and offers valuable insights for designing bioinspired materials.

Acknowledgments: This work was supported by Polish National Science Centre grant no. 2016/22/E/NZ1/00656 to AN. The studies were performed in the NanoFun laboratories co-financed by ERDF within the Innovation Economy Operational Program POIG.02.02.00-00-025/09.

Co-authors: Anna Krztoń-Maziopa (Warsaw University of Technology)

Abstract: Electrorheological (ER) elastomers are intelligent composite materials whose mechanical properties can be dynamically adjusted using electric fields, making them well-suited for use in soft robotics, adaptive vibration control, and flexible sensing technologies. This research focuses on the design and analysis of ER elastomers enhanced with electroactive particles. These particles, chosen for their high dielectric properties, are embedded within a polymer-based elastomer matrix to boost the material's ER response. 

In the course of this work, ERE (electrorheological elastomer) samples were developed using a PDMS (polydimethylsiloxane) matrix combined with core-shell electroactive particles. The core of these particles consisted of an anionic ion exchange resin (PSt/DVB-CH₂-NR₃⁺A⁻) which is basically polystyrene/divinylbenzene copolymer coated with a thin layer of the conductive polymer poly(3-n-octylthiophene) (P3OT), doped with iron (III) chloride. Samples were prepared with varying mass fractions of the core-shell particles 1%, 3%, and 5% to the PDMS. Cross-linking of the samples was performed both with and without the application of an electric field of 0.5 kV/mm. A series of rheological tests was then conducted, revealing that the synthesized elastomers demonstrated characteristic ERE behavior.

The experimental part was primarily devoted to analyze the electrorheological properties of the EREs with different amount of filler contents. Therefore, the samples were prepared and with the help of parallel plate (plate-plate) rheometer, the electrorheological measurements were performed. The ER effect was quantified by measuring the change in shear modulus under applied electric fields. Findings reveal that, the type and amount of electroactive filler play a critical role in determining the electromechanical behavior of the elastomers. This work provides key insights into how composition influences performance in ER elastomers, supporting the future development of customizable materials for advanced technological applications.

Acknowledgments: Warsaw University of Technology

Co-authors: Sahrish Batool Naqvi (University of Wrocław), Damian Śnieżek (University of Wrocław), Dawid Strzelczyk (University of Wrocław), Mariusz Mądrala (University of Wrocław), Maciej Matyka (University of Wrocław)

Abstract: We will present our recent results on the nonlinear effects of gravity-driven fluid flow through a two-dimensional, moderately low-porosity, packed bed of stubby stone grains in Darcy, and post Darcy regimes. We focused on preferential channel formation, tortuosity, spatial distribution of kinetic energy,  and vortex formation. We show that nonlinear effects dominate at relatively high Reynolds numbers, even though the deviation from Darcy's law is not visible in friction factor measurements.

A backward-flow fraction $\rho^{-}$ captures the earliest formation and growth of recirculation zones; the participation number $\pi$ increases monotonically, indicating a progressive delocalization of kinetic energy; and tortuosity $\tau$ exhibits a non-monotonous trend—initially flat/slightly decreasing, then rising in the inertial regime. The apparent permeability decreases with $Re$. These results explain why friction-factor-only indicator can obscure the onset of inertial effects in the real porous rocks with moderate porosity, lower than of those studied previously and identify $\rho^{-}$ as an early, robust indicator of recirculation. We further notice an increased asymmetry of the flow field revealed by vorticity analysis and surprising correlation between tortuosity and apparent permeability in the inertial flow regime.

Main reference: https://arxiv.org/abs/2505.10418

Acknowledgments: Funded by National Science Centre, Poland under the OPUS call in the Weave programme 2021/43/I/ST3/00228. This research was funded in whole or in part by National Science Centre (2021/43/I/ST3/00228).

Co-authors: Meteusz Chwastyk (Institute of Physics, Polish Academy of Sciences),  Midhun Mohan Anila (Institute of Physics, Polish Academy of Sciences), Marek Cieplak (Institute of Physics, Polish Academy of Sciences)

Abstract: Phase separation underlies the formation of biomolecular condensates such as stress granules and nucleoli. Constructing a temperature–density-dependent phase diagram is essential for identifying the conditions that enable their formation. To this end, we investigated van der Waals fluids using molecular dynamics simulations and developed different complementary approaches: based on clustering analysis, and on thermodynamic observables such as specific heat and surface tension. By applying the SPACEBALL algorithm to calculate cluster volumes and densities, we extracted binodal and spinodal lines across a wide range of temperatures and densities. Our results yield a consistent critical temperature (T* ≈ 1.31) and show strong agreement with theoretical expectations.

These methods offer a practical framework for mapping phase behavior in systems lacking a defined equation of state, providing valuable tools for studying liquid-liquid phase separation in protein solutions, including those associated with neurodegenerative diseases.

Acknowledgments: The authors acknowledge Professor Marek Cieplak for encouraging research on liquid-liquid phase separation. We gratefully acknowledge Poland’s high-performance Infra- structure PLGrid ACC Cyfronet AGH for providing computer facilities and support within computational grant no plgal- phasyn2.

Co-authors: Anna Maciołek (Institute of Physical Chemistry, Polish Academy of Sciences), Araki Takeaki (Kyoto University), Piotr Nowakowski (Ruđer Bošković Institute)

Abstract: It has been experimentally shown that a micrometer-sized Janus particle, half coated with a photosensitive material and suspended in a near-critical binary solvent, moves spontaneously when illuminated with low-intensity light. Since then, such light-activated self-propellers have been extensively used to study active matter. Although the self-propulsion mechanism of these systems is already quite well understood, very little is known about the behavior of these particles near substrates and in confined geometry, where wetting properties may play the role. Here we address these issues theoretically, using a mesoscopic description, the so-called Fluid Particle Dynamics method, which takes into account both diffusion and hydrodynamics.

Acknowledgments: National Science Centre Poland: funding, Max Planck Institute for Intelligent Systems: computational power

Co-authors: Franciszek Myck (University of Warsaw), Radost Waszkiewicz (Institute of Physics, Polish Academy of Sciences), Łukasz Białas (University of Warsaw), Michał Dzikowski (University of Warsaw), Piotr Szymczak (University of Warsaw), Maciej Lisicki (University of Warsaw)

Abstract: Brewing espresso presents a rich physical system for investigating fluid flow through porous media under pressure. In this process, hot water is forced through a compacted puck of ground coffee, often modeled using Darcy’s law, which predicts a linear relationship between pressure and flow rate. However, coffee is a complex, reactive medium that swells, dissolves, and rearranges during brewing, making the situation far from ideal. Realistic brewing conditions typically involve high pressures (6–11 bar), raising questions about the validity of simple Darcy-based models. We present new experimental measurements and a developed theoretical framework describing the pressure–flow relationship during espresso extraction.

At low pressures (2–5 bar), we observe a linear increase in flow rate, consistent with Darcy’s law. At higher pressures (>5 bar), however, the flow rate saturates and even slightly decreases, indicating a clear deviation. We propose that this nonlinearity results from microstructural changes in the coffee bed under mechanical stress, such as pore collapse or compaction. These findings suggest that standard porous flow models may be insufficient to capture behavior under high-pressure brewing conditions. They highlight the need for new constitutive models tailored to espresso extraction and contribute to a broader understanding of pressure-driven transport in deformable and reactive granular media.

Acknowledgments:

Co-authors: Bartosz Różycki (Institute of Physics, Polish Academy of Sciences)

Abstract: Adhesion of cell membranes arises from the binding of receptor proteins to ligands in the apposing membrane and is central to many biological processes. We apply a statistical–mechanical model and Monte Carlo simulations to explore adhered membranes where receptors and ligands interact with lipid rafts—dynamic nano-scale clusters enriched in sphingolipids and cholesterol. Our results show that raft–raft attraction enhances receptor–ligand binding, while receptor–ligand binding redistributes lipid rafts and increases their co-localization with receptors. These findings provide insight into the interplay between membrane adhesion and raft organization, advancing the understanding of how lipid rafts contribute to biological  processes like cell signaling and immune responses.

Acknowledgments: National Science Center of Poland 2021/40/Q/NZ1/00017

Co-authors: Piotr Szymczak (University of Warsaw), Zhaoliang Hou (China University of Geosciences Beijing), Anna Neubeck (University of Uppsala)

Abstract: Mineral dendrites are an example of a pattern that forms in rocks when they are infiltrated by Mn-rich hydrothermal fluids. These fluids interact with oxygenated fluids within the rock matrix, leading to the formation of manganese oxide, which subsequently precipitates and forms intricate patterns. Bacteria can catalyze manganese oxidation reaction by at least 2-3 orders of magnitude and hence their presence can play a significant role in the formation and growth of manganese precipitates. We hypothesize that presence of Mn-oxidizing bacteria can also trigger band formation in the growing dendrites, which is observed in some natural structures. We investigate this process using numerical simulations and analyze dependence of dendrite morphology on various physical parameters such as initial concentrations of manganese ions and oxygen molecules, reaction rates, nucleation thresholds, and surface energy. We have compared numerical results with experimental data on 3D dendrites in zeolites obtained using X-ray microtomography, which has revealed the presence of a banded pattern. Simulation results and experimental data agreement allows us to infer the presence of microorganisms during formation. We have compared numerical results to morphologies of the real systems with the aim of reconstructing hydrochemical conditions prevailing during their growth.

Acknowledgments: The project is financed from the state budget, allocated by the Minister of Science under the "Perły Nauki II" Program.