Direct detection of molecular intermediates from first-passage times

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Science Advances  01 May 2020:
Vol. 6, no. 18, eaaz4642
DOI: 10.1126/sciadv.aaz4642
  • Fig. 1 Transport in controlled potential landscapes.

    (A) Illustration of the proposed link between first-passage time distributions and a particle moving across a potential landscape. (B) Typical experimental image. (C) Experimental 2D probability distribution of particle positions for a channel with four optical traps. The color bar indicates the total number of times a particle is observed at a position within the channel. (D) 1D potential landscape, U(x), calculated from the probability distribution in (C) with potential minima depth ΔU ~ 3 kBT. Channel exits are indicated by solid lines and the boundaries between minima as dashed lines. Minima labels L(R) 0 to 3 indicate the lowest number of minima that must be crossed to exit to the left (right) reservoir, for a particle starting in this minimum.

  • Fig. 2 First-passage time distributions of colloidal particles in imposed potential landscapes.

    Distributions in (A) and (B) show P(tFPT) on a linear and log-log scale for particles diffusing over a potential landscape with minima depth ΔU ~ 3 kBT. Dashed lines indicate the predicted power-law scaling according to Eq. 1 and the value of m for each distribution corresponds to the number of minima crossed by the particle. (C) P(tFPT) for particles crossing two potential minima (m = 2) of different depths, ΔU, as indicated. Vertical dashed lines indicate the time scale over which the first-passage time (FPT) distributions exhibit a linear regime on a log-log scale, as defined by the black dashed lines. (D) The length of the power-law (linear) regime as a function of potential minima depth for all colloidal systems.

  • Fig. 3 First-passage time distributions from the mesoscale to the microscale.

    (A) P(tFPT) for the colloidal channel system. (B) P(tFPT) for the nanoscale, molecular hopper, system comprising a DNA oligonucleotide ratcheted through an α-hemolysin pore. m = 1 and m = 2 distributions are shown for crossing one or two states (making two or three hops, respectively). (C) P(tFPT) for the folding and unfolding dynamics of two DNA hairpin systems with different structures and thus energy landscapes.

Supplementary Materials

  • Supplementary Materials

    Direct detection of molecular intermediates from first-passage times

    Alice L. Thorneywork, Jannes Gladrow, Yujia Qing, Marc Rico-Pasto, Felix Ritort, Hagan Bayley, Anatoly B. Kolomeisky, Ulrich F. Keyser

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