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Abstract: When analyzing single-molecule data, a low-dimensional set of system observables typically serve as the observational data. We calibrate stochastic dynamical models from time series that record such observables (our focus throughout is on a molecule's end-to-end distance). Numerical techniques for quantifying noise from multiple time scales in a single trajectory, including experimental instrument and inherent thermal noise, are demonstrated. The techniques are applied to study time series coming from both sim… Show more

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Cited by 23 publications
(95 citation statements)
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References 86 publications
(95 reference statements)
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“…2B. Our observations support the view that a tethered polypeptide samples its PMF with a diffusion coefficient of D eff ∼ 10 3 nm 2 ∕s, which is in surprisingly close agreement with previous measurements using tethered proteins (14)(15)(16)(17)(18).…”
Section: Resultssupporting
confidence: 92%
“…2B. Our observations support the view that a tethered polypeptide samples its PMF with a diffusion coefficient of D eff ∼ 10 3 nm 2 ∕s, which is in surprisingly close agreement with previous measurements using tethered proteins (14)(15)(16)(17)(18).…”
Section: Resultssupporting
confidence: 92%
“…A white measurement noise was assumed [21]. This information was used in conjunction with likelihood based methods to estimate quantities describing the ξ dynamics.…”
Section: Methodsmentioning
confidence: 99%
“…Our primary interest is modeling time series associated with single-molecule simulations/experiments [1, 2, 3, 4, 5, 6, 7, 8, 9]. We demonstrate how information in such time series can be summarized into scatterplot data [8, 10] and how a new method introduced here, the P-splines using Derivative Information (PuDI) method, can be used to gain better quantitative understanding of these time series containing information about multiple time scales in situations where the dynamics are homogeneous or an external force causes the stochastic evolution rules to be time inhomogeneous.…”
Section: Introductionmentioning
confidence: 99%