Molecular Dynamics
Prof. Martin Zacharias
Research Field
The function of proteins and nucleic acids in living systems is strongly coupled to the molecular motion and dynamics of these biomolecules. Our group uses computer simulation methods to study the structure, function and dynamics of biomolecules. Our goal is to better understand structure formation processes and to elucidate the mechanism of ligand-receptor association in atomic detail. As the main computational technique we employ Molecular Dynamics simulations based on a classical force field to follow molecular motions including the surrounding solvent and ions. This allows us to extract thermodynamic and kinetic properties of the biomolecular system using methods of statistical mechanics. We also develop computational docking approaches to predict how proteins interact with other proteins or RNA and DNA molecules or how small drug-like compounds bind to biomolecular targets.
Address/Contact
Ernst-Otto-Fischer-Straße 8/I
85748 Garching b. München
+49 89 289 12393
Fax: +49 89 289 12444
Members of the Research Group
Professor
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
Prof. Dr. | Martin | Zacharias | 046 | +49 89 289-12335 |
Office
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
Sonja | Ortner | 047 | +49 89 289-12393 |
Scientists
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
M.Sc. | Shu-Yu | Chen | 042 | +49 89 289-12564 | ||
M.Sc. | Maximilian | Kienlein | 044 | +49 89 289-12730 | ||
Brianda | Lopez Santini | 045 | +49 89 289-12731 | |||
Dr. | Patrick | Quoika | 048 | +49 89 289-13766 | ||
Dr. | Maria | Reif | 045 | +49 89 289-12731 | ||
M.Sc. | Carlos Christian | Sustay Martinez | 040 | +49 89 289-51612 | ||
M.Sc. | Luis | Vollmers | 044 | +49 89 289-12730 | ||
M.Sc. | Paul | Westphälinger | 044 | +49 89 289-12730 | ||
Dr. | Gabriel | Zoldak | 130 | – | ||
M.Sc. | Richard | Zschau | 042 | +49 89 289-12564 |
Students
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
B.Sc. | Maximilian | Block | – | – | ||
Asha | Knipp | – | – | |||
B.Sc. | Pawel | Korzeb | – | – | ||
B.Sc. | Mira Tanja | Mahlein | – | – | ||
B.Sc. | Yasmin | Saremi Nanji | – | – | ||
Luis Jakob | Walter | – | – | |||
Ziyi | Wang | – | – |
Other Staff
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
Dr. | Jonathan | Coles | 048 | – | ||
Susmita | De | – | – | |||
M.Sc. | Christina | Frost | – | – | ||
Margrethe | Gaardlos | – | – | |||
Ameya | Harmalkar | – | – | |||
M.Sc. | Julian | Hartmann | 701 | – | ||
Dr. | Manuel | Hitzenberger | 048 | +49 89 289-13766 | ||
Dr. | Korbinian | Liebl | – | +49 89 289-13697 | ||
Anshuman J. | Mahapatra | – | – | |||
M.Sc. | Danial | Pour Jafar Dehkordi | 059 | – | ||
B.Sc. | Arrien Symon | Rauh | – | – | ||
Jose | Roldan | – | – | |||
Prof. Dr. | Philipp | Scherer | 073 | – | ||
Neelanjana | Sengupta | – | – | |||
Till | Siebenmorgen | 059 | – |
Teaching
Course with Participations of Group Members
Current and Finished Theses in the Group
- DNA Stability Estimations by Alchemical Free Energy Simulations
- Abschlussarbeit im Bachelorstudiengang Physik
- Themensteller(in): Martin Zacharias
- Mechanism of Protein-DNA and Protein-Peptide Binding Studied Using Advanced Sampling Simulations
- Abschlussarbeit im Masterstudiengang Physik (Biophysik)
- Themensteller(in): Martin Zacharias
- Molecular Dynamics Study of Substrate Processing by gamma-secretase
- Abschlussarbeit im Masterstudiengang Physics (Applied and Engineering Physics)
- Themensteller(in): Martin Zacharias
- Study of Biomolecule Folding and Binding Using Molecular Dynamics and Markov State Modeling
- Abschlussarbeit im Masterstudiengang Physik (Biophysik)
- Themensteller(in): Martin Zacharias
- Prediction of the binding geometry of a membrane protein complex
- Abschlussarbeit im Bachelorstudiengang Physik
- Themensteller(in): Martin Zacharias