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b'Although thermophoresis, i.e. the directed movement of molecules in a temperature gradient, was discovered more than 150 years ago, its molecular origin is not jet fully understood. Nonetheless thermophoresis is used as a principle in biomolecular binding measurements. Both topics are interesting and worth a scientific discussion. In this thesis, systematic experiments over a large parameter space were conducted. From these measurements a combination of different theories about its molecular origin could be verified. Thus, the first result of this thesis is that the phenomenon thermophoresis consists of different additive contributions. Some of them relate to the ionic nature of the molecule and are non-existent when the molecule is electrically neutral. The microscopic mechanism of these ionic contributions to thermophoresis is discussed in the first part. It continues the work on the capacitor model and explains a further contribution, which we call Seebeck effect in analogy to solid state physics. Through the different contributions we bridge the gap between local thermodynamic equilibrium approaches and non-equilibrium theories. Several applications will greatly benefit from understanding the molecular physics of thermophoresis. Pharmacological screens are conducted to determine the binding affinity of a whole molecular library to a target molecule and thus to identify the best candidates for a new drug. These screens will be improved when thermophoresis can be predicted and for example the influence of the buffer can be determined. Binding measurements of biomolecules can already be conducted in cell lysate. The second part of this thesis will show thermophoresis measurements inside living cells for the first time. This paves the way for in vivo binding measurements inside cells. To make thermophoresis measurements compatible to cell culture, the setup was changed in great parts, now using total internal reflection fluorescence (TIRF) microscopy.'