1

Evolutionary algorithms as a tool for designing chemical computers

Jerzy Gorecki

Peter Dittrich (Jena University, Germany)
Andy Adamatzky (University of West England, United Kingdom)

Current status: Information processing with different types of chemical media has been studied for a long time. It is expected that chemical information processing devices can be reduced to nano-scale & work autonomously. Therefore, chemical computers seem to fit specific applications like intelligent nano-materials, smart drugs or deep space sensors where mass, and size reduction is crucial. Typical chemical information processing devices are constructed as networks of communicating nonlinear elements. There are many factors, e.g. character of nonlinear medium, type of communication or the geometry of interactions between processing elements that should be taken into account to design a device performing a specific function. Currently, chemical information processing devices are constructed with bottom-up approach: simple elements (e.g. logic gates) are invented & more complex operations are realized by concatenation of simple operations. We plan to develop algorithms that can optimize a selected complex structure of communicating nonlinear elements in order to achieve its max. functionality with respect to a specific information processing task. Inspiration for this PhD topic comes from the publications co-authored by J. Gorecki and P. Dittrich (Phil. Trans. R. Soc. A 373 (2015) 20140219;, International Journal of Neural Systems, 25, (2015), 1450032).

The goal: To write evolutionary algorithms that optimize the functionality of a given network of communicating chemical nonlinear elements for a specific information processing task.

Our approach: The project is multidisciplinary and covers: the evolutionary algorithms, information theory, theory of nonlinear processes, chemical kinetics & computer simulations of nano-scale systems with complex chemical reactions. Bearing in mind the problem complexity, we would like to apply the evolutionary algorithms to the automatic design. The fitness function optimized within the evolution will measure the mutual information between the system evolution and the expected answer of the device.

2

Effect of fluctuations in biological processes confined in nanoscale organs

Bogdan Nowakowski

Annie Lemarchand
University Pierre and Marie Curie, France

Current status: The influence of fluctuations in biological systems has become a subject of intensive investigations since the rapid development of bioengineering and biochemical processing. Internal fluctuations may be an especially important issue in biological processes which are often restricted to nanoscale domains, where intrinsic stochastic perturbations reach a relatively higher level. Moreover, biochemical reactions are governed - as a rule - by nonlinear dynamics, which is particularly sensitive to even small perturbations of the average, deterministic evolution. In development processes, like genetic reproduction or cell differentiation, minor errors at the nanoscale are known to lead to significant phenotypical misexpressions. Inspiration for this PhD topic comes from the publication co-authored by B. Nowakowski and A. Lemarchand in J Chem Phys., 137, 074107 (2012)) and from the publication of B. Nowakowski group (J Chem Phys., 141, 124106 (2014)).

The goal: The present study should analyse in detail the robustness of dynamics to random perturbations, with focus on possible occurrence of morphogenesis mutations and metabolism malfunctions.

Our approach: The study will include (i) a theoretical approach with approximate (possibly analytical) calculations, (ii) simulations at different description levels: from deterministic scale to particle scale through stochastic, mesoscopic scale. Selection of the systems should be done in collaboration with a bioengineering company.

3

Mechanism of nanostructure formation and surface engineering for activated materials in catalysis

Juan Carlos Colmenares Q.

Roger Glaeser
Leipzig University, Germany

Current status: The growing concerns related to petroleum-based chemicals, together with environmental and health regulations, indicate the necessity of clean and sustainable technologies development for pollution abatement and energy. In the last decade, most of those technologies relayed on catalysis with a growing interest in active photocatalytic material applications. Until now, several studies showed correlation of photocatalyst morphology with its activity and selectivity in selected process, i.e. underlying the effects of photocatalyst preparation method, operating conditions, and reagents composition. New photocatalytic nanocomposites of high activity, selectivity, stability and sustainable costs are sought. Therefore, design of photocatalysts which can selectively operate under different conditions (e.g. light sources, solution pH, etc. ) without activity drop would be beneficial, enhancing potential application perspectives in new and retrofit industrial installation (photoreactors). Understanding the photocatalyst surface composition, chemical, electronic and morphological transformations of an active phase, as well as active sites arrangement and distribution are of huge importance to optimize the photocatalytic material and thus better control the whole photocatalytic process. Inspiration for these studies comes from the publications of Colmenares group: Advanced Functional Materials (Inside Cover Page), 25(2) (2015) 221–229; ChemSusChem, 8 (2015) 1676–1685.

The goal: The design of multicomponent intelligent nano-photocatalytic systems showing enhanced activity in processes such as biomass-based derivatives transformation, selective photocatalysis or emission control. The project aims at investigating how the performance of nanostructured photocatalytic materials (nano-: spheres, fibers, tubes, rods or wires) correlates with their surface composition and active sites distribution.

Our approach: Photocatalytic materials will be prepared using different techniques, including co-precipitation, impregnation, and sonication methods. Several techniques will be applied for physico-chemical characterization, e.g. X-ray photoelectron spectroscopy, X-ray diffraction, high resolution transmission electron microscopy. Additionally, infrared or ultraviolet–visible spectroscopy can be applied to describe precisely the nature of surface species. In order to investigate materials activity and selectivity in selected processes, the student will conduct research under UV-Vis activation using standard and homemade photocatalysts, and applying conventional flow/batch photoreactors under atmospheric pressure using well defined reagents mixtures and mass spectrometer and/or gas chromatograph as online products analyser. The Ranido (catalyst manufacturer, Czech Republic) is willing to collaborate on this project.

4

Molecular imprinting for selective determination of chosen food toxins

Wlodzimierz Kutner

Francis D'Souza
University of North Texas, USA

Current status: In natural recognition mechanisms, complicated biomolecular assemblies are involved. Although this recognition (exploited in biosensors) is mostly specific, the biomolecules suffer from low stability under harsh working conditions. Therefore, artificial recognition systems capable of mimicking recognition functions of corresponding biomolecules are synthesized. Molecularly imprinted polymers (MIPs) are among them. For MIP preparation, first, pre-polymerization complex of dedicated functional monomers and an analyte, initially used as the template, is formed in solution. Next, this complex is polymerized while encapsulating template molecules inside the resulting MIP. Subsequent extraction of the template vacates molecular cavities complementary in their size and shape to the template molecules. That way, a MIP ready for selective recognition exploiting well-defined molecular mechanisms with different types of analyte binding is fabricated. Inspirations for this PhD topic come from the publications co-authored by W. Kutner and F. D'Souza: Biosens. Bioelectron., 2013, 41, 634–641; Biosens. Bioelectron., 2015, 74, 960–966.

The goal: Devising and fabricating MIPs to serve as recognition units of chemical sensors for selective determination of chosen food toxins.

Our approach: We will focus on chemosensing of food toxin analytes incl. representative antibiotics, steroids, heteroaromatic amines, and nitrosamines. Each analyte will require preparing different functional monomers. However, all monomers will share the same electrochemically very conveniently polymerizing thiophenne moiety. Therefore, the student shall electropolymerize a pre-polymerization complex to result in a thin MIP film on a conducting transducer for transduction of a chemical recognition signal into that electric analytically useful. The research will involve: (i) designing, synthesizing, and characterizing new dedicated redox functional and cross-linking monomers capable of electropolymerization, (ii) preparing and characterizing thin MIP films for sensing applications, and (iii) fabricating and testing the chemosensors, featuring MIP recognition units, under flow analytical conditions. The Affinisep (formerly Polyintell; France) and MicruX Technologies (Spain) SMEs will be attracted to commercialize products of the research proposed herein.

5

Secondary organic aerosol formation: kinetic and chemical studies of aqueous-phase reactions of selected plant volatiles in nanodroplets

Rafal Szmigielski

Irena Grgic
National Institute of Chemistry, Slovenia

Current status: Secondary organic aerosols (SOA) are air-suspended liquid or solid particles having aerodynamic diameters of less than 10 micrometers and a complex chemical composition. These systems have been the subject of intense multidisciplinary research for the last two decades, as aerosol nanoparticles affect human health, the quality of life and the Earth’s climate. Despite great scientific efforts, our understanding of nanoparticles formation and growth in ambient air, as well as of their processing, is far from thorough elucidation. Volatile plant metabolites belonging to the terpenoid family, including isoprene (C5H8), its oxygenates, monoterpenes (C10H16), and oxygenated aromatics, play a key role in such processes. Owing to unsaturated bonds, these species serve as SOA precursors, being involved in the chain of numerous reactions with atmospheric oxidants, including hydroxy radicals, sulphate radicals and ozone. Although a number of these reactions are not recognized, their unknown products, incl. organosulphates, organonitrates, and nitroxyorganosulphates, add to the aerosol mass and enhance the hydrophilic properties of atmospheric aerosol nanoparticles. Inspiration for this PhD topic comes from the publication co-authored by R. Szmigielski and I. Grgic in Chemical Reviews, 115(10), 3919, (2015) and from the publication of I. Grgic group in Environmental Science & Technology, 49(15), 9150. (2015).

The goal: To recognize the aqueous-phase reactions of selected plant volatiles at the molecular level through off-line and on-line mass spectrometry techniques and kinetic analysis.

Our approach: Experiments envisage application of atmospheric ionization mass spectrometry as a key tool to monitor the reaction course between a selected plant volatile and the atmospheric oxidant, and to compare these results with the analysis of ambient SOA samples collected at various sites. The unknown SOA components that appear at considerable concentrations in the LC/MS traces of aqueous-phase simulation experiments and ambient SOA samples will be characterized using a detailed interpretation of mass spectra, organic synthesis of reference material, kinetic analysis and DFT-based calculations. Obtained data should be of value for the modelling community, helping to improve their air quality models and the models of pollution dissemination in the lower troposphere. The data may also be used by agencies dealing with air monitoring, and in particular - monitoring of air-impacted by non-negligible biomass burning episodes.

6

Investigation of lateral distribution of components in biological membranes

Wojciech Gozdz

Ales Iglic
University of Ljubljana, Slovenia

Current status: Biological membranes are multicomponent two dimensional fluids. The phospholipids form a bilayer where many different components such as proteins or hydrocarbons are embedded. The behaviour of proteins in biological membranes is still not sufficiently understood. Biological functions of proteins may be modified by their local concentration. The shape of the membrane may depend on the local concentration of components but also the concentration of components may be influenced by the membrane curvature. Inspiration for these studies comes from the publication co-authored by W. Gozdz and A. Iglic in PLoS ONE 8(9) , e73941, (2013) and from publication of W. Gozdz group in J. Chem. Phys., 137(1), 015101, (2012).

The goal: To better understand the physics of multicomponent biological membranes, and to elucidate, how the distribution of different kinds of components influences membrane properties and biological functions, related to differences in the local concentration of components. To describe (experimentally and theoretically) the interaction of biological membranes with nanoparticles and nanostructured surfaces, with the possible application in biomedicine.

Our approach: We will construct and investigate free energy functionals where the geometry of the biological membrane will be taken into account. Such approach combines knowledge from: physics (statistical mechanics), mathematics (differential geometry), biology (lipid membranes & biological cells), material science (fabrication of nanostructures), and computer science (numerical minimization, low level programming).We plan the collaboration with a Slovenian company Sensum d.o.o. (www.hellotrade.com) on the automatic determination of blood cell shapes for diagnostic purposes.

7

Effects of confinement on ionic liquids

Alina Ciach

Enrique Lomba
The Institute of Physical Chemistry "Rocasolano", Spain

Current status: Ionic liquids have properties determined by long-range Coulomb interactions, and by the short-range specific potential. Room temperature ionic liquids in porous electrodes are potentially important to innovative electrochemistry. In particular, they are promising for the development of supercapacitors. Transport of ions under confinement has relevance for ionic devices in domains like biophysics, biosensors, on-a-chip laboratories or artificial cells. Thermodynamic, structural, & dynamic properties of ionic liquids/ionic-liquid mixtures near charged surfaces & in porous media are not sufficiently understood. In particular, to date there is no theory able to describe correctly the phase behaviour of confined ionic liquids. Difficulties in theoretical modelling are due to special inhomogeneities & long-range correlations. Inspiration for this PhD topic comes from the papers of E. Lomba group in J. Phys.: Condens. Matter 27 (2015) 194127, and A. Ciach group in Soft Matter, 8, 3567 (2012).

The goal: To describe, with theoretical & simulation methods, the structural, thermodynamic, mechanical & dynamic properties of ionic liquids & ionic liquid mixtures, for various degrees of confinement.

Our approach: The PhD student will perform theoretical, numerical & simulation studies in collaboration with the ROCASOLANO Institute in Madrid. (S)he will participate in developing software for graphics processing units commercialised by a company Sistemas Inormáticos Europeos S.A:U (clustersie.com).

8

Smart Tips: Droplet Microfluidic Chips-on-Tips Directly Operable with Automatic Pipettes

Piotr Garstecki

Roland Zengerle
University of Freiburg, Germany

Current status: The techniques of droplet microfluidics have been rapidly developing since 2001. After almost 15 years of research it is possible to execute chemical & biochemical reactions and incubation of microorganisms in nanolitre reactors. There are two major directions of use of these techniques in analytical chemistry and medical diagnostics. The first uses the ability to split liquid samples into thousands or millions of identical micro-droplets and to i) run digital assays that provide absolute quantitation of DNA or immuno-protein targets, and ii) sort large libraries of random mutations either of DNA (e.g. coding enzymes), or plasmids in living bacterial cells. The second direction uses much smaller number of droplets, each prepared with a different chemical composition to execute either a number of different assays, or dilution assays, such as the most commonly used i) quantitation of bacterial load in physiological samples, and ii) antibiotic susceptibility testing. The techniques of droplet microfluidics, however, are still not widely used. The spread of this technology is hampered by the requirement of sophisticated microfluidic instrumentation. Inspiration for this PhD topic comes from the paper of P.Garstecki group in LAB ON A CHIP, 13, 20, 4096-4102 (2013) and R. Zengerle group: ANALYST, 139, 11, 2788-2798 (2014).

The goal: The aim of the PhD project is to develop droplet microfluidic chips that could be operated with the simplest and most common laboratory equipment, i.e. with an automatic pipette. The student will develop systems for i) generation of libraries of identical droplets, ii) generation of libraries of double droplets, and iii) execution of an antibiotic susceptibility test.

Our approach: Expertise of the Garstecki research group and of the Zengerle laboratory will be used for the execution of basic operations on droplets, and initial work on execution of a dilution assay on a chip operated with a pipette, to develop microfluidic systems directly interfaced with an automatic pipette. We will promote short internships of the student in the high-tech startup companies (Scope Fluidics and/or Curiosity Diagnostics at the IPC, and BioFluidix in Freiburg). These activities will facilitate potential transfer of the results to industry.