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Prof. Dr. Martin Zacharias

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+49 89 289-12335
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Molecular Dynamics
Job Title
Professorship on Molecular Dynamics

Courses and Dates

Title and Module Assignment
Free Energy Simulations in Soft Matter and Biomolecular Physics
Assigned to modules:
VI 2.5 Zacharias, M.
Assisstants: Reif, M.
Mon, 09:00–17:00, PH 1151
Theoretical Biophysics
Assigned to modules:
VO 2 Zacharias, M.
Assisstants: Reif, M.
Fri, 10:00–12:00, PH HS2
Seminar on current topics in molecular biophysics
Assigned to modules:
HS 2 Zacharias, M. Wed, 14:00–16:00, CPA EG.006B
Exercise to Theoretical Biophysics
Assigned to modules:
UE 2
Responsible/Coordination: Zacharias, M.
Biomolecular Systems
Assigned to modules:
SE 2 Gerland, U. Simmel, F. Zacharias, M. Thu, 12:00–14:00, PH 3343
FOPRA Experiment 74: Molecular Dynamics (AEP, BIO)
course documents current information
Assigned to modules:
PR 1 Chen, S.
Responsible/Coordination: Zacharias, M.
Lab course biophysics for students of biochemistry
eLearning course
Assigned to modules:
PR 4 Bausch, A. Dietz, H. Lieleg, O. Rief, M. Simmel, F. … (insgesamt 7) Wed, 08:00–13:00, PH 3024

Offered Bachelor’s or Master’s Theses Topics

Computersimulation der Bindung von Peptiden an RNA
RNA molecules are involved in many processes in cells. Typically, these processes involve the interaction with proteins and peptides. There are specific short peptide segments that often mediate the interaction between proteins and RNA. In the BSc thesis project the binding of short tripeptides with a central Arginine residue (often part of RNA binding peptides) and RNA will be studied using Molecular Dynamics simulations. Aim is to identify and characterize the preferred binding sites on the RNA molecules. It is hoped that it will allow the prediction of how and where larger proteins (that contain such short RNA binding motifs) bind to RNA molecules.
suitable as
  • Bachelor’s Thesis Physics
Supervisor: Martin Zacharias
Molekulare Simulation der Faltung von Amyloidstrukturen
Natural proteins typically form stable globular structures. However, approximately 30% of natural proteins do not adopt a single stable structure but adopt a so called disordered state. Disordered proteins but also mutated globular proteins can aggregate to form regular amyloid structures. Such structures are involved in many diseases. In the BSc-project a computational methodologyto predict the amyloid structure of protein sequences will be developed and tested. The method is based on including information extracted from known amyloid structures to guide molecular dynamyics simulations.
suitable as
  • Bachelor’s Thesis Physics
Supervisor: Martin Zacharias
Untersuchung der Flexibilität von Amyloidstrukturen mit MD-Simulationen
Amyloid structures can form by aggregation of misfolded protein molecules or peptides. These aggregates are involved in several diseases. The various amyloid structures differ in the conformational flexibility and stability. Very flexibile amyloid structures are more likely to disaggregate and can be recognized and eliminated by proteases and immune molecules. Aim of the BSc thesis is to investigate the conformational flexibility and dynamics of different amyloid structures using computer simulations and to understand the physical origin of the dynamics of amyloid structures.
suitable as
  • Master’s Thesis Biophysics
Supervisor: Martin Zacharias
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