Single molecule force spectroscopy at high data acquisition: A Bayesian nonparametric analysis

Ioannis Sgouralis, Miles Whitmore, Lisa Lapidus, Matthew J. Comstock, Steve Presse

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Bayesian nonparametrics (BNPs) are poised to have a deep impact in the analysis of single molecule data as they provide posterior probabilities over entire models consistent with the supplied data, not just model parameters of one preferred model. Thus they provide an elegant and rigorous solution to the difficult problem encountered when selecting an appropriate candidate model. Nevertheless, BNPs' flexibility to learn models and their associated parameters from experimental data is a double-edged sword. Most importantly, BNPs are prone to increasing the complexity of the estimated models due to artifactual features present in time traces. Thus, because of experimental challenges unique to single molecule methods, naive application of available BNP tools is not possible. Here we consider traces with time correlations and, as a specific example, we deal with force spectroscopy traces collected at high acquisition rates. While high acquisition rates are required in order to capture dwells in short-lived molecular states, in this setup, a slow response of the optical trap instrumentation (i.e., trapped beads, ambient fluid, and tethering handles) distorts the molecular signals introducing time correlations into the data that may be misinterpreted as true states by naive BNPs. Our adaptation of BNP tools explicitly takes into consideration these response dynamics, in addition to drift and noise, and makes unsupervised time series analysis of correlated single molecule force spectroscopy measurements possible, even at acquisition rates similar to or below the trap's response times.

Original languageEnglish (US)
Article number123320
JournalJournal of Chemical Physics
Volume148
Issue number12
DOIs
StatePublished - Mar 28 2018

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data acquisition
Data acquisition
Spectroscopy
Molecules
spectroscopy
molecules
acquisition
traps
tethering
time series analysis
time signals
Time series analysis
dwell
dynamic response
beads
Dynamic response
flexibility
Fluids
fluids

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Single molecule force spectroscopy at high data acquisition : A Bayesian nonparametric analysis. / Sgouralis, Ioannis; Whitmore, Miles; Lapidus, Lisa; Comstock, Matthew J.; Presse, Steve.

In: Journal of Chemical Physics, Vol. 148, No. 12, 123320, 28.03.2018.

Research output: Contribution to journalArticle

Sgouralis, Ioannis ; Whitmore, Miles ; Lapidus, Lisa ; Comstock, Matthew J. ; Presse, Steve. / Single molecule force spectroscopy at high data acquisition : A Bayesian nonparametric analysis. In: Journal of Chemical Physics. 2018 ; Vol. 148, No. 12.
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