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Department of Physical Chemistry

List of available PhD theses

Ab initio photodynamics in condensed phase: Method development and applications

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Study programme: Chemistry (Czech language)

Annotation

Computational photodynamics is a fast evolving field. At present, we are able to simulate ultrafast porcesses in medium-sized molecules. This Thesis focuses on developement and applications of photodynamical methods describing light-induced processes in condensed phase. For more information, see http://photox.vscht.cz/

Ab initio simulations of structural, thermodynamic and transport properties of metalorganic frameworks

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: Ing. Ctirad Červinka, Ph. D.

Automated study of photochemical mechanisms

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The thesis will focus on mechanisms of organic reactions in both the ground and excited states. Ab initio techniques and methods of ab initio molecular dynamics will be used. It is anticipated that new computational techniques will be developed, in attempt to automatize the search for key aspects of reaction mechanisms.

Benchmarking classical and quantum-mechanical molecular simulations for predictions of phase equilibria

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: Ing. Ctirad Červinka, Ph. D.

Benchmarking the ab initio methods for polymorph stability ranking for molecular crystals

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: Ing. Ctirad Červinka, Ph. D.

Biosensors methods for environmental monitoring and food safety

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

Nowadays, industrial activity produces vast amounts of harmful chemicals that can pollute the environment and contaminate food, posing a serious challenge to public health. The development of analytical methods for rapid and sensitive detection and quantification of harmful chemicals is an important and timely research topic. The dissertation will focus on the development of biosensors for rapid and sensitive detection of selected low molecular weight analytes, which present risk to water and food quality. Mainly, the work will focus on optical biosensors based on surface plasmon resonance (SPR) and potentially also on their combination with electrochemical methods for more complex sample analysis. In particular, the work will include the development of functional layers for affinity capture of selected analytes and the development of detection assays and methodologies enabling rapid and sensitive detection of analytes in complex matrices. The developed biosensing approaches will be evaluated in model experiments and the results will be compared with those obtained using conventional analytical methods.

Computational electrochemistry: Developement of new methods and applications

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The Thesis focuses on developement of new apprroaches for charge transfer modelling. The work includes both the charge transfer between molecules as well as the charge transfer between a molecule and electrode. Modern approaches based on ab initio molecular dynamics will be used. For more information, see http://photox.vscht.cz/

Determination of vapour pressures of environmentally important high-boiling compounds

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Study programme: Chemistry (Czech language)

Annotation

The vapor pressure is one of the most frequently measured thermodynamic properties for pure organic compounds. Measurements are relatively easy for low boiling compound (e.g. components of gasoline) and precise data can be found in handbooks and databases. On the other hand, measurements of high boiling compounds such as polyaromatic hydrocarbons or phthalates represents challenging task and existing data are scarce and associated with high uncertainty, which prevents reliable modelling of fate of these chemicals in the environment. Non-commercial apparatuses assembled in our laboratory enable measurement in subpascal pressure region; methodology of thermodynamically controlled extrapolation developed by us enables reliable vapor pressure determination in sub-millipascal pressure region. The work will focus on determination of vapor pressures for a group of polyaromatic hydrocarbons listed in the USA EPA Priority List of Pollutants, as a part of our cooperation with several European laboratories.

Development of methods for studying extremely low vapor pressures

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Study programme: Chemistry (Czech language)
Theses supervisor: Ing. Vojtěch Štejfa, Ph.D.

Electrochemistry of van Hove singularities in two-dimensional crystals

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: Mgr. Otakar Frank, Ph.D.

Annotation

The PhD candidate will develop the methodology required to investigate the discontinuities in the density of electronic states (so-called van Hove singularities) in two-dimensional crystals and their heterostructures. The project will include the preparation of the materials (graphene, transition metal dichalcogenides like MoS2) by exfoliation or transfer, preparation of electrodes, and in-situ Raman and photoluminescence spektroelectroelectrochemical investigation coupled with electric transport and electron transfer measurement.

Gas and liquid transport study in graphene oxide and carbon nanotubes based membranes

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Study programme: Chemistry (Czech language)
Theses supervisor: doc. Ing. Karel Friess, Ph.D.

Annotation

Membrane separation processes (MSP) belong to the modern technologically significant separation methods. Furthermore, MSP are less economical demanding and more eco-friendly industrial processes compared to the conventional separation techniques used in chemical, petrochemical, pharmaceutical and food industries. The most significant industrial applications of MSP for gas separation are focused on separation of helium from natural gas, separation of hydrogen from hydrocarbons, carbon monoxide or nitrogen and also for removing carbon dioxide from biogas or organic vapors from air. Generally, graphene oxide (GO) based membrane materials belong to the modern and dynamically growing group of materials that have many interesting properties. Especially, this work will be targeted on GO based separation of hydrogen from carbon dioxide. Besides, the separation effect of prepared membranes will be tested for the selective removal of organic contaminants from the water. Our laboratory is focused on the topic of membrane separation for more than 15 years. Currently, we participate in two grant projects of the GA CR aimed at increasing the efficiency of membrane separation processes. This doctoral thesis is thematically linked to these projects.

Machine Learning in Computational Spectroscopy

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Study programme: Chemistry (Czech language)

Annotation

Artificial intelligence and machine learning approaches have recently witnessed a massive development in various fields of science and technology. In the suggested thesis, the candidate will apply these techniques into the field of computational spectrsocopy with a focus on electronic spectroscopies. For more information, see http://photox.vscht.cz

Modeling of ultrafast processes in radiation chemistry

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The enormous experimental development allows for a direct study of electron photoemission from water and solutions. New, hithertho unknown phenomena have emerged. The Intermolecular Coulomb Decay represents one example. The new phenomena can give rise to novel spectroscopies or to application in radiooncology. The proposed Thesis will focus on the exploration of these phenomena, using the methods of quantum theory of molecules and molecular simulations. For more information, see http://photox.vscht.cz/

Modelling of nuclear quantum effects in spectroscopy

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The Thesis will focus on method development for simulations of spectral properties with a special attention paid to the nuclear quantum effects. The role of nuclear quantum effects on molecular structure and thermodynamics will be explored, too. For more information, see http://photox.vscht.cz.

Molecular Simulations of Atmospheric Aerosols

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

Atmosphere of Earth is a unique chemical reactor. Light induced reactions play a prominent role in the intiation of many important chemical reactions. Many of the atmospheric processes also take place within heterogeneous processes, e.g. on the surface of aerosols or dust particles. The project focuses on theoretical modeling of chemical and photochemical processes in the stratosphere and in the troposhere. The whole toolbox of theoretical methods will be used within the project. For more information, see http://photox.vscht.cz/

Molecular simulations of electrode-electrolyte interface

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The thesis will focus on theoretical study of the interfaces between the electrode material and electrolytes. Extremely concentrated electrolytes will be studied as well, especially in the context of novel energy sources. The work will include techniques of quantum chemistry and statistical mechanics. For more information, see http://photox.vscht.cz/

New effective separation membranes for water and wastewater treatment based on hybrid carbon-based materials

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: doc. Ing. Karel Friess, Ph.D.

Annotation

Current membrane separation processes allow efficient purification and physical disinfection of water from undesirable components on the basis of a size-sieving mechanism without the need for chemical agents. The pore sizes and their distribution on the membrane surface is an important factor for the effective removal of contaminants and microorganisms. The thesis will study the possibilities of using newly prepared membrane materials based on carbon materials (carbon nanotubes, graphene derivatives, etc.) with targeted surface modifications (eg doping with antimicrobial agents, etc.) in order to effectively remove collected contaminants from water. In addition to the preparation, characterization and testing of materials, the work will also include modelling of the separation process. The result of this work will be, besides the preparation of an effective separation material and describing the model, an extension of knowledge in the given membrane field.

New nanostructured carbon nanotubes-based composite membranes for selective gas separation

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Study programme: Chemistry (Czech language)
Theses supervisor: doc. Ing. Karel Friess, Ph.D.

Annotation

Membrane separation processes (MSP) belong to the modern technologically significant separation methods. Furthermore, MSP are less economical demanding and more eco-friendly industrial processes compared to the conventional separation techniques used in chemical, petrochemical, pharmaceutical and food industries. The most significant industrial applications of MSP for gas separation are focused on the separation of helium from natural gas, separation of hydrogen from hydrocarbons, carbon monoxide or nitrogen and also for removing carbon dioxide from biogas or organic vapours from the air. Generally, single-wall carbon nanotubes (SWCNT) and graphene oxide (GO) based membrane materials belong to the modern and dynamically growing group of materials that have many interesting properties. Especially, this work will be targeted on SWCNT-GO-based separation of hydrogen from carbon dioxide or from other gases. Our laboratory is focused on the topic of membrane separation for more than 15 years. Currently, we participate in two grant projects of the GA CR aimed at increasing the efficiency of membrane separation processes. This doctoral thesis is thematically linked to these projects. The thesis will be focused on the study of theoretical and experimental aspects of the transport of gases and their mixtures in GO and polymer-based membranes.

New polymers for membrane separations of difficultly separable mixtures

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Photochemical processes in astrochemistry

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The Thesis will focus on processes initiated by light in various astrochemically relevant molecules and system. In particular, the applicant will study ice particles and the role of high-energy radiation in astrochemistry. For more information, see http://photox.vscht.cz.

Preferential interactions of osmolytes with soft matter

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: RNDr. Mgr. Jan Heyda, Ph.D.

Annotation

Protein stability and association, membrane formation, solubility of chemically heterogeneous drugs and their partitioning between inner and outer cell environment are theoretically simple to describe, but in reality complex processes, which play an essential role in soft matter. These processes can be seen as results of competition of several driving forces [Dill]. More commonly, these forces compensate each other and are very finely balance at system equilibrium. Another approach to insight, and subsequent control of these processes employs the perturbation of the natural environment by the addition of cosolvents. These interactions might be net-attractive or net-repulsive, leading to enrichment or depletion of the additive in solute vicinity. However, the manifestation is different for small (osmotic properties) and large solutes (dialysis, partitioning), thus to obtain a generic view is rather challenging. In this thesis, the candidate will research the changes in chemical potential of various solutes in the presence of osmolytes and the implications on the solute state, i.e., conformation or phase [Heyda, Chudoba]. The investigation thus cover systems form single small molecules to monomer and similar polymer, up to macromolecular complexes, which naturally require employment of whole ensemble of theoretical approaches. On the simulation side, all-atom molecular dynamics simulations will be complemented by implicit solvent coarse-grained models [Chudoba, Roux]. Monte-Carlo simulations will be used for investigation of phase equilibria employing highly coarse-grained models. Simulation data will be complemented by statistical thermodynamic framework [Smith, Smith1], with the long term aim of derivation theory-based equations of state.

Structure and reactions of solvated electron

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

Solvated electron is an interesting redox species. Hydrated electron, i.e. the electron solvated in water, is a short living transient species (picosecond lifetime). It turns out that the solvated and presolvated electron play a major role in radiation damage of biomolecules and in atmospheric chemistry. The subject of the proposed Thesis is the interaction of high energy radiation and the research of solvated electron fomration and reactivity. For more information, see http://photox.vscht.cz/

Tailoring metallic nanoparticles for specific plasmonic enhancement

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The focus of the work will be on assembly of plasmonic nanoparticles and fluorescent nanoparticles using DNA origami. Metal nanostructures are capable of massive enhancements of optical response, which arise from collective electromagnetic resonances called plasmons. The PhD work will consist of characterization of plasmon resonance (bulk and single particle) of metallic nanoparticles, DNA functionalization of plasmonic nanoparticles and optimization of the process of their self-assembly to desired orientation. Developed assemblies will serve to study spatial manipulation of light by plasmons.

Tailoring of nanostructure in mixed matrix membranes for selective removal of CO2 from biogas

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: doc. Ing. Karel Friess, Ph.D.

Annotation

Membrane separation processes belong to modern technologically important separation methods, which are less demanding (economically and ecologically) in comparison with classical separation methods. For the gas separation applications, mainly polymer membranes are used. Their performance (permeability or separation effect) can be additionally adjusted by the targeted embedding of liquid or solid additives into the polymer matrix. The dissertation thesis will focus on the preparation, characterization, and testing of the so-called mixed matrix membranes for the separation of gases based on glassy polymers and functional nano-additives with a purposefully prepared structure. In addition, modeling of the separation process will be part of the work. The result of this work will be prepared and tested membrane material for the effective removal of CO2 from biogas and extension of knowledge in the given membrane field.

Theoretical investigation of electron transfer processes in bio-organometallic complexes

Department: Department of Physical Chemistry, Faculty of Chemical Engineering
Theses supervisor: RNDr. Mgr. Jan Heyda, Ph.D.

Annotation

Electron transfer processes play a central role in number of signalling and catalytic processes, which are vital for human life as well as for utilization in bio-inspired nanotechnology. Their theoretical investigation presents a challenging task, as it implicitly involves multiple electronic states and spam over several spatial- and temporal scales (femtoseconds to subnanoseconds). In this thesis, the candidate will employ state of the art ab-initio TD-DFT calculations in explicit solvent QM/MM setups within GPU-accelerated TERACHEM quantum calculation package to study the relaxation and time propagation of the system. At the initial laser irradiation, or near state-crossing geometries the adiabatic approximation breaks down. In order to gain an insight in these non-adiabatic events, SHARC quantum chemical package will be employed. Research stays in the group of prof. Gonzales (University of Vienna), developers of the SHARC software, are assumed. Theoretical results will be complemented by unique time-resolved spectroscopic data (prof. Vlček). Computational resources at local highly accelerated GPU-cluster and at national supercomputer infrastructure (IT4I) will be demanded and used.

Thermodynamic non-ideality in membrane separations

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The topic of the doctoral thesis is to study the key principles influencing membrane separations of liquids.

Visualization with plasmonic nanoparticles using single molecule microscopy techniques

Department: Department of Physical Chemistry, Faculty of Chemical Engineering

Annotation

The focus of the work will be on evaluating the magnitude of the fluorescence shifts and enhancement of plasmon-coupled fluorophores using single molecule localization microscopy and time-resolved single molecule spectroscopy. Single molecule localization microscopy overcomes the diffraction limit by calculating the center positions of a fluorescent spot based on the known point spread function of the optical microscope. While plasmonic coupling is known to strongly increase number of emitted photons from a fluorophore, it also appears to affect the position of the emission. The work will consist of visualization of assembled fluorophores with and without a plasmonic nanoparticles, data analysis and statistics.


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