the absence of externally applied force (as might be applied via magnetic or optical tweezers).

The aims of this article are to: (1) review how data acquisition and data analysis affect TPM measurements; (2) explain a practical scheme of data selection and quantify the fractions of typical data that are rejected by each of our criteria; (3) calibrate particle motion, tether length and observation time so that subsequent TPM experiments can be quantitatively interpreted; and (4) discuss the physical processes that govern TPM. Calibration of the particle motion allows precise predictions of how a particular conformational change of the tether, such as Lac repressor induced looping of DNA, affects TPM.

Some of our experimental results were outlined in [@nels07a]. Theoretical work leading up to the present results on TPM motion appeared in [@sega06a; @Nelson2006; @Towles2008]. For example, Segall et al. predicted effects of changing the size of the bead and tether length, which we document experimentally in the present work. Our results are preparatory to experimental [@han?cLength] and theoretical [@Towles2008] work on DNA looping in the *lac* operon system.

![\[fig:TPM\] Idea of the tethered particle motion method. Cartoons showing the tethered bead in the (a) absence and (b) presence of 