Since 2005, my research has concentrated on three main theoretical domains:
Quantum Chemistry (Electronic Properties of Semiconducting Molecules and Nanocrystals)3:
Theoretical Study of Electronic Structure and Excited States, Spectroscopic Analysis and Vibronic Coupling Effects, Charge Transport Properties in Organic Molecules and Inorganic Nanowires; with applications in: Organic Electronics, Photovoltaic Devices, Nanotechnology.
Computational Biology (Therapeutic Targeting)2:
Epigenetic Regulation and Chromatin Remodeling Mechanisms, Molecular Interactions and Structure-Based Drug Design.
Biological Physics (Mathematical Modeling and Collective Dynamics of Soft Matter)1:
Self-Assembly and Biomechanics of Cytoskeleton, Collective Motion and Pattern Formation in Biological Systems, Stochastic Population Dynamics and Ecological Modeling, Non-Equilibrium Thermodynamics and Polymer Physics of Solutions and Gels, Active Liquid Crystals in Biological Systems, with applications in: Self-Organizing Systems, Polymeric Devices, Biotechnology.
1- Since joining the Department of Biological Physics of the Max Planck Institute for the Physics of Complex Systems (MPI PKS), I have focused on developing mathematical models and computational algorithms to study systems exhibiting pattern formation and collective motion. My work includes modeling and predicting the dynamic behavior of such systems over time. One major project involved simulating active liquid crystals as a model for the length- and shape-controlled meiotic spindle—a large bipolar assembly of motor proteins and microtubules during cell division. This multipurpose software models the Brownian dynamics of rigid and semiflexible rods, incorporating stochastic processes that describe nucleation, polymerization, and depolymerization. The core code, written in FORTRAN 2003 (over 30,000 lines), is parallelized using OpenMP, and communicates with VMD through a Tcl interface to visualize simulation results. The models have also been applied to study stochastic population dynamics in biological and non-biological self-organizing systems.
In addition, I contributed to the ESF-Nachwuchsforschergruppe “Chem-IT” at the Center for Advancing Electronics Dresden (cfAED). This project aimed to characterize the mechanical properties of smart gels (e.g., PNIPAAM) for chemical information processing devices, particularly chemical transistors. I extended the Flory-Huggins model for polymer solutions by incorporating the elastic term of the Flory-Rehner theory to describe hydrogel swelling, developing predictive models for how environmental factors such as alcohol concentration and temperature affect behavior. These systems function as self-controlling valves in chemical transistor structures for 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 Department of Neuropathology of the University Hospital of Tübingen, I studied ligand–protein interactions using molecular dynamics and docking to evaluate the effects of compounds—such as polyphenols, histone deacetylase inhibitors, and salvinorin A—on potential therapeutic targets (receptors, enzymes, etc.) in neurological disorders, including oncogenesis, neurodegeneration, and psychiatric conditions. I also developed computer programs using classical Monte Carlo simulations and steepest descent optimization to model patterns of histone acetylation in response to drugs, alongside the distribution of HDACs across brain regions. Network analyses of drug-targeted proteins in neurodegenerative diseases complemented these studies.
3- My earlier research focused on the electronic structure, vibrational properties, vibronic couplings, photoluminescence, optical absorption, ionization, and geometry optimization of organic and inorganic molecules and clusters, including silicon nanocrystals, benzofluorene, pentacene, benzo(ghi)perylene, naphthalene, benzene, metal-phthalocyanine, and PTCDA. These studies, conducted in collaboration with experimental groups in Chemnitz, Jena, and Kiel, supported applications in organic electronics, photovoltaics, and nanotechnology, using ab initio and semi-empirical methods (DFT, TD-DFT, CIS(D), RI-CC2, MP2, DFTB, ZINDO). I also contributed to projects on the electronic transport properties of organic and inorganic materials—such as polyacetylene, polypyrrole, and quantum point contacts of copper and gold—using NEGF-DFT and gDFTB methods, alongside modeling resistivity in thin metal films and nanowires through extensions of the Mayadas-Shatzkes model.
Last update: May 1, 2014