Offered topics of bachelor/master theses 

We currently offer several topics of bachelor/master theses (see below) in the field of computational thermodynamics. The theses can be written either in English or Czech. In brief, the work behind the offered theses includes literature surveying, performing computational studies, and evaluating and interpreting the obtained results with respect to various computational assumptions applied.

The theses are intended as part of our current grant projects, so the student(s) may get paid.

If interested, please contact Drs. Ctirad Červinka or Martin Klajmon

Molecular simulations of the properties of biocompatible ionic liquids

Annotation: Biocompatible ionic liquids (BILs) combine suitable physicochemical, environmental, and biological properties. They are applied e.g. in biomedical and pharmaceutical fields, because they can increase both the solubility of drugs and their potential to penetrate the cell membrane. To find the optimal BIK for a given medical purpose, knowledge of the thermodynamic and structural properties of a wide range of different BIL candidates is essential. Since the experimental determination of all necessary data is labor- and cost-intensive, the application of predictive computational approaches appears to be a suitable alternative that would screen potential candidates at a fraction of the time and cost required by experiments. Such computational procedures are particularly computer molecular simulations. This work aims to determine the properties of selected BILs using molecular dynamics simulations and to evaluate the accuracy and predictive power of these methods by means of a comparison with available experimental data. In particular, surface-active BIKs will be the subject of interest. In this computationally-oriented work, the student will learn how to professionally prepare and run molecular simulations on National Supercomputing Center (IT4I) machines and evaluate their results. The work is also part of a grant project funded by GAČR. 

Effect of conformational flexibility and atomic polarizability on the properties of condensed molecular systems

Annotation: Computational molecular simulation methods (e.g. molecular dynamics and Monte Carlo simulations) are an important source of information about the systems under study, and could ideally replace time-consuming and expensive laboratory experiments. One of the key factors for accuracy and reliability in predicting macroscopic thermodynamic properties (e.g., enthalpies of phase transitions) using simulations is a sufficiently long simulated trajectory and a sufficiently accurate force field. The notion of a simulated trajectory can be thought of as the acquisition of a sufficient number of different "snapshots" of the molecular system under consideration from which a reliable picture of its behavior can be constructed, while the force field is responsible for the accuracy of the calculated interaction energies in these "snapshots". Increasing the accuracy in each of these aspects usually means increasing the time required for the simulations. This work aims to study and determine the effect of the force field components of complex molecules, which are related to conformational flexibility and atomic polarizability, on the accuracy of the results obtained, and to what extent the description of these effects can be simplified or even neglected. For example, in the case of Monte Carlo simulations, the high conformational flexibility of complex molecules often leads to a significant increase in the required computational time, but on the other hand, it is essential for the description of sublimation and polymorphism of molecular crystals. In this computationally-oriented work, the student will learn how to professionally prepare and run molecular simulations on National Supercomputing Center (IT4I) machines and evaluate their results. In particular, the focus will be on polycyclic organic semiconductor systems in condensed phases. The work is also part of a grant project funded by GAČR. 

Thermodynamic properties of porous liquids from computer simulations  

Annotation: The work aims to gain thermodynamic properties of selected porous liquids using molecular dynamics simulations in the LAMMPS or TINKER software. The student will learn to work with these simulation software tools, to process the obtained simulation results, and will carry out her/his own computer simulations the purpose of which will be to evaluate the accuracy of the obtained data with respect to various simulation approaches applied (e.g., the use of nonpolarizable/polarizable force field). The work is also part of a grant project funded by GAČR. 

Prediction of molecular parameters of the PC-SAFT equation of state using quantum mechanics

Annotation: Molecular parameters of the advanced PC-SAFT equation of state are routinely determined by fitting them to experimental data. However, in order to increase the predictive power of this model, it is also possible to determine the parameters in a more theoretical way using quantum mechanical methods. This computationally-oriented work aims to implement and apply the recently proposed quantum mechanical technique SEPP [Kaminski and Leonhard, J. Chem. Eng. Data 2020, 65, 5830] to estimate the PC-SAFT parameters and to evaluate their potential for estimating thermodynamic properties of systems containing, e.g., dipolar non-protogenic solvents or pharmaceuticals.