Physics of Biological Systems: From Molecule to The Cell

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Achievements of this research can be summarized in three parts.1.One of the focuses in this research was collapsing transition of DNA. In order to explore a single molecular dynamics of DNA molecule, we developed double-beam laser tweezers and micro-fluidic cell in which ionic solution could be exchanged during force measurement. By using that apparatus, we measured mechanical response of collapsed DNA under the presence of multivalent cation, Spermidine(SPD3+). We found nonlinear response, such as plateau and stick-release pattern in force-extension curve. Those reflect the coexistence of collapsed state and elongated state of DNA along the arc length. We also found reentrant collapsing transition of single molecular DNA, implying that collapse DNA becomes coiled state again at very high concentration of SPD. Paper was published.2.We also worked on the problem of genetic networks. How far the mathematical model can predict the dynamics of the cellular process is the fundamental questi … More on in biophysics. For that purpose, we synthesized a simple genetic network module consists of a positive feedback, and measured its dynamics by using reporter system with Green Fluorescence Protein (GFP). The time course of the gene expression after the initiation of the genetic switch was measured and compared with mathematical model. Biophysical parameters of the reactions were determined by the independent experiments. We found that the positive feedback module makes a response delay compared with non-feedback system. The response function and the delay time agreed well with the prediction from the model. Paper has been submitted for publication.3.We developed an Atomic Force Microscope to explore the unfolding dynamics of single molecular protein. SNase was used as a simplest protein to test the unfolding process. Highly nonlinear, stick-release type response was observed when we stretch SNase. The number and height of the peaks in force extension curve has strong correlation with pulling speed of AFM, which may reflect reaction kinetic paths of folding and unfolding processes. This project is still going on. Less