Research Topics

Since 2005, my research has been focused on theoretical studies in three main fields:

Biological Physics | Soft Matter Physics1:

• • Physics of the Cytoskeleton

  • Polymer Solutions and Polymer Gels

  •  Active Liquid Crystals

  • Collective Motion and Pattern Formation

  • Stochastic Population Dynamics

    • Methods: Mathematical Modeling, Statistical Physics, Brownian Dynamics, Classical Monte Carlo, Coarse-grained Molecular Dynamics, Thermodynamics, and Hydrodynamics.

Bioinformatics | Computational Biology2:

• • Molecular Interactions and Drug Design

  • Pharmacokinetics and Pharmacodynamics

  • Epigenetics

    • Methods: Mathematical Modeling, Statistical Physics, Classical Monte Carlo, Molecular Docking, Protein Structure Prediction, Iterative Optimization Methods, Sorting Methods, Data Mining, and Networks Analysis.

Quantum Chemistry | Physics of Semiconductors3:

• • Theoretical Study of Electronic, Spectroscopic, Vibronic, and Charge Transport Properties of Organic Molecules and Nanoscale Materials

    • Methods: DFT, TD-DFT, CIS(D), RI-CC2, MP2, DFTB, ZINDO, NEGF-DFT and gDFTB, and All-atom Molecular Dynamics

1- Since joining the MPI PKS

, I have worked on developing mathematical models and proper computer algorithms, for studying different systems with pattern formation and collective motion. I have also done mathematical modeling for predicting the behavior of such systems over the time. The project was initially defined for simulating active liquid crystals as a model for studying the length- and shape-controlled meiotic spindle, a huge bipolar assembly of motor proteins and microtubules, which are polymerizing proteins with a cylindrical structure, during the cell division. This multipurpose program works based on Brownian dynamics of rigid / semiflexible rods, in a framework of several stochastic processes which explain their nucleation, polymerization, and depolymerization. The core part of the software has been written in FORTRAN 2003, containing over 30,000 code lines and parallelized with OpenMP. Through a Tcl interface, the software is able to communicate with VMD in order to demonstrate parts of the results. The developed models are also used for studying the stochastic population dynamics in biological and non-biological systems with self-organizing behaviors.

Besides, I have been involved in one of the projects of ESF-Nachwuchsforschergruppe “Chem-IT” of the Center for Advancing Electronics Dresden (cfAED 

). The aim of the project is the characterization of the mechanical properties of smart gels, e.g. PNIPAAM, for the development of chemical information processing devices, especially the chemical transistors with the focus on thermodynamic description of the volume phase transition and the swelling kinetics of hydrogels. I have studied the swelling process of hydrogels in multi-component solvents by extending the Flory-Huggins model for polymer solutions through addition of elastic term of the Flory-Rehner theory of rubber swelling, and developed mathematical models for predicting the behavior of this system due to the environmental changes, e.g. alcohol concentration and temperature. The studied systems act as self-controlling valves in chemical transistor structures for designing lab-on-chip devices, with applications in medicine and information technology. 

2- In collaboration with the Division of Immunopathology of the Nervous System of the Institute of Neuropathology of the University Hospital of Tübingen

, I have worked on ligand–protein interactions with molecular dynamics and molecular docking techniques in order to study the effects of different chemical compounds (e.g. polyphenols, histone deacetylase inhibitors, salvinorin A) on receptors, enzymes, etc. as potential targets for therapeutic development in various neurological disorders, from oncogenesis, to neurodegenerative and psychiatric disorders. Besides, I have developed computer programs based on classical Monte Carlo and the steepest descent optimization method in order to perform computer simulations describing the patterns of histone acetylation in response to medical drugs, along with the distribution of HDACs in different brain regions. I have also analyzed the networks of the drug targeted proteins in neurodegenerative diseases.

3- My previous studies are related to the calculations of electronic structure, vibrational properties, vibronic couplings, photoluminesence, optical absorption, ionization, and geometry optimization in organic and inorganic molecules and clusters (e.g. silicon nanocrystals, benzofluorene, pentacene, benzo(ghi)perylene, naphthalene, benzene, metal-phthalocyanine, and PTCDA), with applications in organic electronics, photovoltaic devices and nanotechnology, using ab-initio and semi-empirical quantum chemistry methods (DFT, TD-DFT, CIS(D), RI-CC2, MP2, DFTB, ZINDO), in collaboration with experimentalists in Chemnitz, Jena, and Kiel. I had also contributions to the projects on electronic transport properties of organic and inorganic materials (e.g. polyacetylene, polypyrrole, and quantum point contacts of copper and gold), using NEGF-DFT and gDFTB methods, along with the study of resistivity in thin metal films and metal nanowires by extending the Mayadas-Shatzkes model and developing proper computer programs.

Last update: May 1, 2014