Research projects

11 scientists from IPC and 18 co-mentors from foreign units will support PD2PI fellows in their indiwidual projects.

The following research projects were selected as a result of the competition procedure:

Project 1

Stationary states out of equilibrium in various physical systems

Dr. Paweł Żuk

Mentor: dr hab. Anna Maciołek

Co-mentor: Prof. Peter Vaughan Elsmere McClintock

Partner organization: Lancaster University

Nonequilibrium thermodynamics is a modern field of science under constant development. Contributions are in high and growing demand since contemporary science sets focus on the processes that in principle happen only out of equilibrium. This is especially pronounced in the crossovers of physics and science disciplines that were once regarded as distinct: chemistry, biology, geology etc.. Here we propose to study a special case of thermodynamic nonequilibrium state: a stationary state, which a physical system can achieve e.g., under a constant external forcing. We are interested in finding and examining an extreme principle that characterizes such system. We propose to focus on the energy of the system instead of the entropy. Especially on the energy fluxes and the excess of energy contained in the system under forcing in comparison to the energy stored in equilibrium. We aim to study three systems in stationary state under external forcing that have different underlying physics: Fermi-Ulam-Pasta-Tsingou model, gas flow in a channel with an obstacle and ionic solution in the vicinity of the oscillatory electrode. All three systems are well understood from the mechanistic perspective and accessible for posing thermodynamic questions. The successful application of the uniform extreme principle in those cases will open a possibility to apply it also to the systems including chemical reactions (chemical processes, energy storage) and possibly even to living organisms.

Project 2

Machine learning design of anion-binding catalysts: chirality transfer of organoreceptors

Dr. Dariusz Piekarski

Mentor: Associate Prof. Adam Kubas

Co-mentor: Prof. José Alemán

Partner organization: Autonomous University of Madrid

This project develops and validates a methodology to predict the chirality transfer in anion-binding (AB) catalysis.
We present a theoretical approach complemented by experimental validation, which combines potential energy surfaces (PES) with molecular dynamics (MD) simulations to obtain the structures and reaction profiles. This strategy will allow identifying the key transition states (TSs) responsible for the formation of the chiral product and required for the further wave function (WF) analysis. Building of an extended database of electronic properties will be performed for the weakly interacting substrates, products and crucial TSs on PES, as well as for host-model guest complexes. We aim to find patterns and then make predictions based on the given organoreceptor - model guest WF similarities. The search for WF similarities will be done with machine learning (ML) techniques in order to learn patterns and predict the efficiency in enantioselectivity transfer of a given anion organoreceptor.
As an initial test for benchmarking the methodology a tetrakistriazole H-donor catalyst and an exemplary halide guest will be used as model system. The stoichiometry of the complexes and the key binding features of the catalyst will be delivered both experimentally and theoretically. A detailed theoretical study of the interactions within the complex will be disentangled and compared with the experimental H-NMR spectroscopy titration experiments. The methodology will be then extended to other organoreceptor's structures, and the similarities between the weak interactions at the binding region of the model catalyst will be compared.
Our procedure also aims to deliver novel anion-binding organoreceptors that can effectively induce enantioselectivity in novel transformations, such as metal-free, formal C-C cross coupling reactions. To achieve that, the proposed methodology will be implemented to design further modifications of the potential catalysts.
To sum up, the use of the similarities analysis in the binding of various organoreceptors to predict its catalytic/enantioselective efficiency might lead to a remarkable technique to modify and test existing supramolecular anion receptors for novel enantioselective applications such as drug discovery.

Project 3

Understanding the mechanism of hole scavenger photo-electrochemical oxidation

on the surface of semiconductor

Dr. Bhavana Gupta

Mentor: Dr. Wojciech Nogala

Co-mentors: Prof. Domen Kazunari, Dr. Kim Mckelvey, Dr. Klaus Mathwig

Partner organizations: University of Tokyo, Trinity College Dublin, University of Groningen

Photo-electrochemical (PEC) water splitting is an elegant way of harvesting solar energy to generate green fuel. Materials used for this purpose suffer with the problem of low efficiency due to inefficient light absorption capacity and charge recombination. To achieve efficient charge separation, an in-depth understanding of the surface property of the photoanode is indeed the need of the hour. Surface of the semiconductor change drastically in the presence of hole scavenger which subsequently reduces charge recombination. However, the mechanism of hole scavenger in PEC oxidation and how the surface influence the hole scavenger electrochemical is scarcely reported in the literature.
We propose to understand the mechanism of different hole scavenger PEC oxidation on the surface of semiconductor film grown by cost effective spray pyrolysis technique. Furthermore, the mechanism study will be supported by various spectroscopic, microscopic and microfluidic concentration estimation technique. The main supporting data of this study will be Scanning electrochemical microscopy (SECM) to acquire microscopic information along with electrochemical study. Theoretical calculation of SECM result will further back the obtained information through the experiment. This study will help in tailoring the surface of semiconductor for the purpose of efficient pure water splitting.

Project 4

Structural mechanics of soft-granular clusters: from simulations

to microfluidic experiments on droplet aggregates

Dr. Michał Bogdan

Mentor: Dr. Jan Guzowski

Co-mentor: Prof. Sauro Succi

Partner organization: Italian Institute of Technology

We intend to study mechanical properties of quasi-2D aggregates of dozens or hundreds of water droplets, very densely packed (up to a volumetric packing fraction of 85- 95%) in a large droplet of oil. The droplet of oil will itself be immersed in an external fluid. We will construct the aggregates by the so-called T-junction microfluidic technique and drain them from excess oil if necessary. We will then compress the cluster and let it relax. By engineering the geometry of the system to be quasi-2D and all water droplets within one plane, we will be able to use video-tracking to map precise movements of individual droplets. We will map rearrangements of the droplets induced by compression of the system, as well as those induced by its relaxation, both while still under compression, and after it has ceased. We will construct numerical models to predict, interpret and rationalize the results. They will be based on the Lattice Boltzmann method. This way, we hope to be able to understand the role of topology and finite system size, as well as other parameters in the dynamics of the system. We will describe and attempt to rationalize the differences between behavior of our aggregates and cell clusters, on which similar experiments have been conducted and reported. We hope this will shed light on principles behind tissue mechanics, apart from helping to answer some fundamental questions on physics of finitely sized emulsions.

Project 5

In silico optimization of trans-cis photoisomerization of retinoids

Dr. Michał Andrzej Kochman

Mentor: Associate Prof. Adam Kubas

Co-mentor: Prof. Leticia González

Partner organization: University of Vienna

9-cis retinoids have potential application in the treatment of some inherited diseases of the eye, such as Leber's congenital amaurosis. Their therapeutic relevance points to the need for an efficient synthetic route which would lend itself to industrial-scale production. Recently, Kahremany and coworkers [Org. Biomol. Chem. 2019, 17, 8125.] have developed a synthetic strategy in which 9-cis retinyl acetate is obtained via the photoisomerization of the readily available all-trans retinyl acetate in solution phase under monochromatic irradiation. The simplicity and catalyst-free nature of this photoisomerization reaction make it an attractive option for the large-scale synthesis of 9-cis retinoids. However, a major drawback is that other isomers of retinyl acetate - namely, the 7-cis and 13-cis isomers - occur as undesired byproducts.
The objective of the present project is to identify the factors which control the product distribution ratio of the photoisomerization reaction, and to predict the optimal choice of experimental conditions for the formation of the desired 9-cis retinyl acetate. To this end, we will simulate the excited-state dynamics of all-trans retinyl acetate as it occurs in the solution phase. The potential energy surfaces of the chromophore will be modelled with a combination of state-of-the-art electronic structure methods and machine learning techniques.

Project 6

Scalable electrosynthesis of dimensionally confined, high purity conducting polymers

at electrified soft interfaces for energy conversion and storage (SOFT-ELECTROSYNTHESIS)

Dr. Bren Mark Felisilda

Mentor: Dsc. Martin Jönsson-Niedziółka

Co-mentor: Dr. Micheál D. Scanlon

Partner organization: University of Limerick

A decarbonised power sector, dominated by renewables, is central to society’s transition to a sustainable energy future. To date, innovative materials chemistry and associated disruptive technologies are at the heart of advances in energy conversion and storage (ECS), like the ubiquitous lithium-ion batteries used in mobile devices, electric vehicles and photovoltaic energy home-scale storage devices. Further breakthroughs in materials design and synthesis, not incremental changes, hold the key to future generations of ECS devices.
SOFT-ELECTROSYNTHESIS will develop an entirely novel platform technology with the game-changing potential to produce high quality, large-scale (beyond square cm), free-floating thin films of pure conductive polymers (CPs), like PEDOT, in a single step and eliminate the use of surfactants or additives. The free-floating films can be transferred to any solid support with ease for device fabrication. The large-scale production of uniformly high-quality CP thin films will be facilitated by the inherent defect-free nature of immiscible liquid-liquid interfaces. The ability to form thin films directly in a single step will eliminate the multi-step nature of creating films by chemical polymerisation and, thus, the requirement for surfactants during processing, e.g., PSS. Interfacial electrosynthesis has the potential to disrupt current industrial methods of producing conducting polymers by combining the key advantages of chemical polymerisation (high dopant contents leading to high conductivity; ease of polymer extraction/scale-up for device integration) and electropolymerisation (direct rapid synthesis of high purity thin films; external control to tune film morphology or thickness).

Project 7

Droplet microfluidic platform for electrochemical monitoring of single cells

Dr. Marcin Szymon Filipiak

Mentor: Dr. Jan Guzowski

Co-mentor: Dr. Cesare Gargioli

Partner organization: Tor Vergata University of Rome

Organ-on-a-chip is a rapidly developing research field in which microfluidics is employed towards encapsulation and culturing of cells in well-defined 3D microenvironment, i.e., on a chip. Coupling of the microfluidic techniques with bioanalytical methods still poses a challenge. Here, we aim at developing new techniques of real-time electrochemical monitoring of single cells. For this purpose we will encapsulate cells in conductive biocompatible hydrogel droplets—so-called “beads”—generated using droplet microfluidics.
A novel polymer mix will be developed consisting of poly(3,4-ethylenedioxythiophene) (PEDOT),
a semiconducting polymer and biocompatible glycosaminoglycan (heparin) allowing for free diffusion of nutrients, metabolites, etc. A device comprising of a bead placed between two electrodes as source and drain contacts together with a reference electrode will yield a new architecture of an organic electrochemical transistor (OECT), capable of sensitive biosensing. Two types of processes will be recorded: conductive polymer doping (electronic mode) and redox reactions (electrochemical mode). Since the beads will contain living cells, after appropriate polymer mix modification, the platform will allow for efficient and selective cell monitoring.
The device will allow to observe immediate single-cell secretome changes upon environmental factors. This will allow deeper insight into micro-physiology and cell heterogeneity. As a proof-of-concept, we will study cardiomyocytes, a first step towards precise in vitro heart disease modelling. The main novelty of the project is the combination of 3D culture methods with multimodal detection for application in drug development and regenerative medicine.

Project 8

Nanoelectrochemistry and fluorescence microscopy:

a combined approach towards single molecule detection

Dr. Steven Linfield

Mentor: Dr. Wojciech Nogala, Dr. Sylwester Gawinkowski

Co-mentor: Prof. Jiří Homola

Partner organizations: Institute of Photonics and Electronics, Czech Academy of Sciences

This project proposes the combined use of bipolar ultramicroelectrodes and fluorescence microscopy to overcome the limitations in the electrochemical detection of single entities. Faradaic processes which involve the passage of currents presently undetectable by state-of-the-art electronics will be used to promote the electrochemical generation of a redox active fluorophore in a second cell. The detection of this fluorophore is not limited by electronics and could be used to resolve `invisible’ electrochemical process, even down to the redox reactions of single molecules. This method will be applied to help elucidate aspects of single entity electrochemistry, including: the processes that occur during the collision of electroactive/catalytic nanoparticles with noble metal nanoelectrodes; the activity of enzymes grafted onto nanoelectrodes during voltammetry; and the difference between the Faradaic processes that occur on Au nanoclusters and bulk Au. By employing this method to better understand the properties of single entities, interesting applications involving single entities can be fully realised.

Project 9

Microfluidic System for Solar Energy Conversion

Dr. Ewelina Magdalena Kuna

Mentor: Associate Prof. Martin Jönsson-Niedziółka

Co-mentors: Prof. Maarten Roeffaers, Prof. Giacomo Bergamini

Partner organizations: Katholieke Universiteit Leuven (KU Leuven), University of Bologna

In recent years, a growing emphasis has been put on the development of clean energy technologies and processes based on renewable energy sources. Solar power is the key to a clean energy future. The sun's energy can be captured to generate chemical or electrical energy via artificial systems that mimic natural photosynthesis. Nevertheless, an integrative challenge of solar-driven technology is transferring the light-fuelled chemical processes from a fundamental proof-of-principle to an exploitable industrial scale. Therefore, the aim of this project is engineering durable and versatile microfluidic devices that can be implemented with catalytic technologies for organic transformations and solar fuels production. It is assumed that the application of microfluidic devices will significantly improve efficiency and reproducibility of photo(electro)catalytic processes and facilitate them scalability.

Project 10

Oxygen Reduction and Hydrogen Evolution catalyzed by Carbon Nitride-Metal

Chalcogenide Composites at Liquid-Liquid Interfaces

Dr. Malik Dilshad Khan

Mentor: Prof. Marcin Opallo

Co-mentor: Prof. Hubert Girault

Partner organization: Ecole Polytechnique Federale de Lausanne

Two of the major concerns the humanity is facing today is energy crisis and the environmental pollution. Currently, the major sources of energy are fossil fuels, which are not sustainable, and are responsible for drastic changes in climate. Therefore, renewable and sustainable sources of energy are highly desired. Oxygen reduction and hydrogen evolution are among the most important reactions for the next generation renewable energy converting systems, but these processes requires suitable catalysts to proceed. The catalysts must have high stability, cost effective, easily scalable for industrial applications and must be environmentally friendly. Carbon nitride is a suitable electrode material, owing to its good electrical properties, lower cost, wider availability and high stability, however the intrinsic low conductivity due to electron hole recombination and slightly high band gap limit its efficiency. The efficiency of carbon nitride can be multifold enhanced by functionalizing carbon nitride with transition metal chalcogenides, due to synergistic effect and band gap tuning. Metal organic precursors (MOP) are well known to produce respective metal chalcogenides and offer more flexibility in preparing binary/multinary metal chalcogenides. Therefore, different MOPs will be used to prepare carbon nitride-metal chalcogenide composites and there catalytic performance for oxygen reduction and hydrogen evolution will be investigated by liquid liquid interfaces.

Project 11

The role of inter-bacteria interaction in antimicrobial resistance – droplet microfluidic

approach to study urinary tract infections

Dr. Ilona Paulina Foik

Mentor: Prof. Piotr Garstecki

Co-mentor: Dr. David Wareham

Partner organization: Queen Mary University of London

To fight increasing antimicrobial resistance (AMR) in urinary tract infection (UTI) is crucial to understand bacterial cell-cell interactions, the influence of pathogen-pathogen and pathogen-nonpathogen interactions on the development of disease and, the role of species inhabiting human urinary tract but not causing UTI.
In this project, we will introduce an innovative approach to study AMR in UTI at a single cell level. By using droplet-based microfluidics we will encapsulate single bacteria cells of various species, pair them in various combinations and investigate the role of bacteria-bacteria interactions in AMR. In our experiments, we will use clinical strains that have already been shown to contribute to the development of UTI or asymptomatic bacteriuria. We will study vertical gene transfer and investigate the conditions at which bacteria targeted by administered antibiotics introduce mutations and become resistant. We will also tackle horizontal gene transfer, focusing on cfDNA, as it may be a potential carrier of antibiotic resistance genes. Finally, we will use innovative mathematical models to investigate the phenotypic heterogeneity using probability distributions of the single cell’s minimum inhibitory concentration, p(scMIC).
In summary, this highly interdisciplinary project will allow for high-throughput screening of bacteria-bacteria interactions providing a better understanding of the mechanisms of resistance in UTI and setting effective treatment strategies.

Project 12

Controlable Belousov-Zhabotinsky vesicles for chemical computing applications

Dr. Frantisek Muzika

Mentor: Prof. Jerzy Górecki

Co-mentors: Associate Prof. Ivan Valent, Prof. Andrew Adamatzky

Partner organizations: Comenius University in Bratislava, University of the West of England

The project is focused on building a chemical computer. Both theoretical and experimental studies are planned. In the theoretical part new types of chemical computing media like enzymatic reactions or catalytic systems will be concerned. However, the main objective of this project is to demonstrate a working prototype of chemical information processing device that executes non-trivial task (beyond a logic gate) and that can operate for a day or more.
Potentially applicable are Belousov-Zhabotinsky (BZ) liquid marbles and media using CHD-BZ system (1,4-cyclohexanedione), which does not produce bubbles in droplet solution. The system will be controlled and stimulated by a potentiostat to provide constant electric field or by an electromagnet generating constant magnetic field.
Another computing platform is based on “silica gardens” grown by hollow metal silicate micro-tubes using a metal catalyst solution (Ru) in a magnetic field. The computing structure will be generated by controllable self-assembling catalyst-rich regions and surrounded by catalyst-free solution of other BZ reagents.
This project will also focus on enzymatic chemical computing. Current experimental systems, when in larger arrays, have interesting parallel-thread performance. The concepts of enzymatic computers will be supported by numerical simulations of coupled enzymatic units based on discrete Turing patterns.

Project 13

Towards the comprehensive real-time monitoring of photoreactions

by the integrated laser/UV-vis-NMR-TR-NUS method

Dr. Kristina Kristinaityte

Mentor: Dr. Tomasz Ratajczyk

Co-mentor: Prof. Ruth M. Gschwind

Partner organization: University of Regensburg

Photochemical reactions are currently of intense interest to scientists as well as researchers in industry, and particularly to the hi-tech and green energy sectors. Further progress in photo science-related fields will depend on a more thorough understanding of the reaction mechanisms of photo processes. The light-based spectroscopies are of primary interest in the characterization of such reactions. Only recently, UV-extended Nuclear Magnetic Resonance (NMR) spectroscopy has been demonstrated to be a very powerful tool for investigation of photo-driven systems. However, further work in this field is necessary to expand the applicability of NMR methods to their full potential. Therefore, the main aim of this proposal is the development of complex spectroscopic technology for comprehensive real-time monitoring of photoreactions. In particular, UV-vis and laser spectroscopy will be integrated with NMR TR-NUS extended spectroscopy. We wish to employ this approach for the monitoring of a few exemplary photoreactions such as the E-Z tautomerism and the light-induced regioselective dimerization of anthracene derivatives, which produces iptycene derivatives. These compounds are of great interest in material as well as applied sciences. Until now, the integrated Laser-UV-vis-NMR-TR-NUS approach has not been demonstrated in the scientific literature. This complex technology has much potential for practical applications.

Project 14

Bimolecular reactions in biological environments: a physicochemical analysis

Dr. José María Carnerero Panduro

Mentor: Associate Prof. Gonzalo Manuel Angulo Núñez

Co-mentor: Dr. Daniel Kattnig

Partner organization: University of Exeter

The intracellular reactions take place in conditions where the diffusion of reactants are a critical step: diffusion is restricted by the presence of large molecules (crowding effect) and the cytoplasm’s complexity topology adds space restrictions to the molecular movement. Numerous theoretical models about bimolecular reactions in biological environments have been developed, but with scarce experimental support. Some heterogeneous systems can mimic these conditions, for example liquid crystals as cellular membrane, no-reactive proteins or nanoparticles as crowding agents or hydrogels as intercellular media; being an excellent way to reproduce chemical reactions in biological conditions.
The purpose of the current project is the experimental characterization and mathematical modeling of kinetic aspects of bimolecular reaction in the aforementioned heterogeneous systems. For that, the experiments will be carried out with biomolecules as proteins or polynucleotides and spectroscopy techniques with the capacity of recording the reaction evolution at very early time stages. The results that could emerge from this work would be essential to the life science and engineering.

Project 15

Vapour-assisted growth of stable 2D/3D hybrid perovskite for solar cell application.

Dr. Rajul Ranjan

Mentor: Prof. Janusz Lewiński

Co-mentor: Prof. Michael Graetzel

Partner organization: Ecole Polytechnique de Lausanne

Energy is one of the major concerns in the growing world. Fossil fuels, nuclear energy etc. are various forms of energy used by modern civilization but they cause pollution, global warming, etc. Solar photovoltaic (PV) is perhaps the most promising clean form of renewable technology to convert solar energy directly into electricity. At the same time, the solar PV market is dominated by Silicon-based solar cell. These crystalline silicon wafers have a thickness in μm range and most of the cost of silicon solar cells is due to the cost of silicon and processing. So there is an imperative need to search for low-cost photoactive materials. 3D Perovskites have proved to be excellent photovoltaic materials, owing to lower exciton binding energy, tunable bandgap, strong light absorption in the visible region and long carriers lifetime. Also, this material utilizes earth-abundant elements and is a low-temperature solution processable. The power conversion efficiency for perovskite solar cells (PSCs) has increased by eight folds in 11 years from ~3 % in 2009 to over 25 % now.

A critical bottleneck to the above prospects for PSCs is their rapid performance degradation when stored under ambient conditions. A commercially successful PV panel needs to withstand the atmospheric conditions over a period of 20-25 years without showing a substantial drop in efficiency. In contrast, the lifetimes of PSCs are extremely low, even with excellent quality of encapsulation. On the other hand, 2D perovskite is moisture stable but has poor optoelectronic properties, thus restricting its sole implementation as an active layer. If 3D perovskite having an outer layer of 2D perovskite can be prepared it will not only increase its stability but could give suitable band alignment for charge transport and hence will increase the stability of these solar cells.