47 citations · 98 across the 5 of their papers we have counts for
5 papers
Calibration of Tethered Particle Motion Experiments
L. Han, B. Lui, S. Blumberg +3
The Tethered Particle Motion (TPM) method has been used to observe and characterize a variety of protein-DNA interactions including DNA looping and transcription. TPM experiments e…
First-principles calculation of DNA looping in tethered particle experiments
Kevin B. Towles, John F. Beausang, Hernan G. Garcia +2
We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted…
Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments
John F Beausang, Philip C Nelson
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regula…
DNA Looping Kinetics Analyzed Using Diffusive Hidden Markov Model
John F. Beausang, Chiara Zurla, Carlo Manzo +3
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to i…
Elementary simulation of tethered Brownian motion
John F. Beausang, Chiara Zurla, Luke Sullivan +2
We describe a simple numerical simulation, suitable for an undergraduate project (or graduate problem set), of the Brownian motion of a particle in a Hooke-law potential well. Unde…