Supervisor: HANTZ, Péter
Co-supervisor: Dr. HORVÁTH, Attila
Phase separation, that is, the formation of high and low density zones inside of an initially homogeneous field with an intermediate concentration of a conserved entity occurs in a series of physical and biological systems. Some interesting aspects of the dynamics of such systems can be modeled by the Cahn-Hilliard equation, or even by reaction-diffusion equations. Practical applications of these (systems of) partial differential equation include phase separation in polymer solutions, dislocation dynamics in solids, formation of ecological patterns, biological morphogenesis, modeling animal skin patterns and many others.
We intend to model the dynamics of defect interactions of colloidal precipitates forming behind a chemical reaction-diffusion front in polyvinyl alcohol gels, previously investigated by PH. Our first goal would be to provide a model and a computer simulation based on a system of reaction-diffusion equations. After this, the Cahn-Hilliard equation coupled to a moving front will be used to model and simulate the phenomenon. Programing skills, a minimal experience in using Linux and some knowledge of numerical methods will be necessary. Later we might perform experiments as well.
Supervisors: Péter HANTZ, PTE AOK Biofizikai Intézet, András BÜKI, InSilico Ltd., and Attila HORVÁTH, PTE TTK Szervetlen Kémia Tanszék
Consultant: István GROMA, ELTE TTK, Institute of Physics
Supervisor: HANTZ, Péter
Co-supervisor: Dr. JAKAB, Ferenc
Phages significantly influence microbial populations by killing bacteria, while they are also considered to be crucial in driving microbial species diversity. In the human intestine, bacterial populations interact and compete with each other, and phages are expected to have a significant role in driving the biodiversity of this complex ecosystem.
Our aim is to analyze the role of bacteriophages in driving the alterations in microflora compositions found in feces of normal and ill (intestinal diseases) samples. Both taxonomy and function analyses will be carried out. In the first step, no DNA isolation and sequencing are planned, we just analyze shotgun sequencing data.
Using appropriate bioinformatics toolkits, CRISPR spacer sequences will be investigated in bacterial genomes. We will identify bacteriophage-specific sequences searching for genes characteristic for bacteriophages (e.g. portal protein, terminase, integrase etc.). In silico host prediction of bacteriophages will be carried out using multiple methods (k-mer frequency, CRISPR protospacer search, direct sequence presence in bacterial genomes etc.). Correlation of bacterial and bacteriophage abundancy will be investigated in healthy and ill patients.
Basic knowledge in computer programing, statistics and the Linux operation system will be required.
Supervisors: Tamás KOVÁCS, Enviroinvest Ltd. Pécs, Péter HANTZ, PTE AOK Biofizikai Intézet, and Ferenc JAKAB, Szentágothai Kutatóközpont
Consultant: János MOLNÁR, TurbineAI
Collaborator: Maria VEHRESCHILD, Goethe University Frankfurt