We systematically studied the potential landscapes of colloidal diffusion systems using the Markov State Model. The potential landscapes includes simulated 1D, 2D, periodical and random potentials, and experimental 2D periodical and random potentials. Robust Perron clustering analysis (PCCA+) identified potential traps successfully. The height of the energy barrier between traps was obtained from the transition rate matrix. The distribution of the height of energy barriers agreed well with that from the Boltzmann distribution of a direct population probability histogram. We were able to evaluate the barrier height with reasonable accuracy without sampling the trajectory at the peak of the barrier directly.

The free diffusion of proteins on live cell membranes is modulated by th...[ Read more ]

We systematically studied the potential landscapes of colloidal diffusion systems using the Markov State Model. The potential landscapes includes simulated 1D, 2D, periodical and random potentials, and experimental 2D periodical and random potentials. Robust Perron clustering analysis (PCCA+) identified potential traps successfully. The height of the energy barrier between traps was obtained from the transition rate matrix. The distribution of the height of energy barriers agreed well with that from the Boltzmann distribution of a direct population probability histogram. We were able to evaluate the barrier height with reasonable accuracy without sampling the trajectory at the peak of the barrier directly.

The free diffusion of proteins on live cell membranes is modulated by the local cellular context both inside and outside the cell. We used an extra-cellular pattern of microgrooves to control the spatial distribution of adhesion complexes on the basal membrane of muscle cells, and evaluated the effects of this topographic patterning on the diffusion dynamics of AChRs. Along the microgroove direction (the x direction), the motion is the same as the anomalous diffusion without the pattern, which can be explained by the dynamic heterogeneity of the diffusion coefficient. In the direction perpendicular to the microgrooves ( the y direction), the motion is hindered and can be modeled as a diffusion with non-constant diffusion coefficient over a 1D periodical potential. This diffusion guided along the y direction is caused by the distribution of integrins.