Change‐Point Localization and Wavelet Spectral Analysis of Single‐Molecule Time Series

Yang, Haw

doi:10.1002/9781118131374.ch9

Cited by 24 publications

(26 citation statements)

References 104 publications

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“…The resulting fit was subtracted from the measured response when indenting vesicles to obtain FDCs. Contact point was determined by using a change point algorithm, 44 and occasionally manually adjusted. Before fitting, FDCs were smoothed (moving average with window length of ∼10 points).…”

Section: Methodsmentioning

confidence: 99%

Competition between Bending and Internal Pressure Governs the Mechanics of Fluid Nanovesicles

et al. 2017

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Nanovesicles (∼100 nm) are ubiquitous in cell biology and an important vector for drug delivery. Mechanical properties of vesicles are known to influence cellular uptake, but the mechanism by which deformation dynamics affect internalization is poorly understood. This is partly due to the fact that experimental studies of the mechanics of such vesicles remain challenging, particularly at the nanometer scale where appropriate theoretical models have also been lacking. Here, we probe the mechanical properties of nanoscale liposomes using atomic force microscopy (AFM) indentation. The mechanical response of the nanovesicles shows initial linear behavior and subsequent flattening corresponding to inward tether formation. We derive a quantitative model, including the competing effects of internal pressure and membrane bending, that corresponds well to these experimental observations. Our results are consistent with a bending modulus of the lipid bilayer of ∼14kbT. Surprisingly, we find that vesicle stiffness is pressure dominated for adherent vesicles under physiological conditions. Our experimental method and quantitative theory represents a robust approach to study the mechanics of nanoscale vesicles, which are abundant in biology, as well as being of interest for the rational design of liposomal vectors for drug delivery.

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Section: Methodsmentioning

confidence: 99%

Competition between Bending and Internal Pressure Governs the Mechanics of Fluid Nanovesicles

et al. 2017

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“…In practice, working with the log of this ratio provided additional computational convenience. Moreover, the threshold value of this log-likelihood ratio corresponding to a 1% false positive rate is easily calculated numerically using a closed-form expression (Yang, 2011).…”

Section: Kinetic Change-point Algorithm and Distribution Constructionmentioning

confidence: 99%

“…To extract detailed kinetic information from complex two-bead observations we developed a novel multi-line fitting procedure inspired by an algorithm developed for modeling fluorescence intensity data (Yang, 2011). …”

Section: Kinetic Change-point Algorithm and Distribution Constructionmentioning

confidence: 99%

Simultaneous Real-Time Imaging of Leading and Lagging Strand Synthesis Reveals the Coordination Dynamics of Single Replisomes

et al. 2016

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. (2016). Simultaneous real-time imaging of leading and lagging strand synthesis reveals the coordination dynamics of single replisomes. Molecular Cell, 64 (6), 1035-1047.Simultaneous real-time imaging of leading and lagging strand synthesis reveals the coordination dynamics of single replisomes AbstractThe molecular machinery responsible for DNA replication, the replisome, must efficiently coordinate DNA unwinding with priming and synthesis to complete duplication of both strands. Due to the anti-parallel nature of DNA, the leading strand is copied continuously, while the lagging strand is produced by repeated cycles of priming, DNA looping, and Okazaki-fragment synthesis. Here, we report a multidimensional single-molecule approach to visualize this coordination in the bacteriophage T7 replisome by simultaneously monitoring the kinetics of loop growth and leading-strand synthesis. We show that loops in the lagging strand predominantly occur during priming and only infrequently support subsequent Okazaki-fragment synthesis. Fluorescence imaging reveals polymerases remaining bound to the lagging strand behind the replication fork, consistent with Okazaki-fragment synthesis behind and independent of the replication complex. Individual replisomes display both looping and pausing during priming, reconciling divergent models for the regulation of primer synthesis and revealing an underlying plasticity in replisome operation. SummaryThe molecular machinery responsible for DNA replication, the replisome, must efficiently coordinate DNA unwinding with priming and synthesis to complete duplication of both strands. Due to the anti-parallel nature of DNA, the leading strand is copied continuously, while the lagging strand is produced by repeated cycles of priming, DNA looping, andOkazaki-fragment synthesis. Here, we report a multidimensional single-molecule approach to visualize this coordination in the bacteriophage T7 replisome by simultaneously monitoring the kinetics of loop growth and leading-strand synthesis. We show that loops in the lagging strand predominantly occur during priming and only infrequently support subsequent Okazaki-fragment synthesis. Fluorescence imaging reveals polymerases remaining bound to the lagging strand behind the replication fork, consistent with Okazakifragment synthesis behind and independent of the replication complex. Individual replisomes display both looping and pausing during priming, reconciling divergent models for the regulation of primer synthesis and revealing an underlying plasticity in replisome operation.3

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“…We employed a variant of time-tagged timeresolved (T 3 R) photon counting 24,25 called time-and polarization-resolved photoluminescence 17,19 to probe directional coupling in isolated TAT crystals. Photons emitted from the sample are sorted into two orthogonal polarization components detected by avalanche photodiodes whose outputs are processed through a high-speed router, thus identifying the arrival time and polarization state of each individual detected photon 17,19 , enabling direct measurement of the time-evolution of polarization contrast with resolution ultimately limited by the timeto-digital converter (4 ps in our implementation).…”

Section: Methodsmentioning

confidence: 99%

Directional Charge Separation in Isolated Organic Semiconductor Crystalline Nanowires

Barnes

2017

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One of the fundamental design paradigms in organic photovoltaic device engineering is based on the idea that charge separation is an extrinsically driven process requiring an interface for exciton fission. This idea has driven an enormous materials science engineering effort focused on construction of domain sizes commensurate with a nominal exciton diffusion length of order 10 nm. Here, we show that polarized optical excitation of isolated pristine crystalline nanowires of a small molecule n-type organic semiconductor, 7,8,15,16-tetraazaterrylene, generates a significant population of charge-separated polaron pairs along the p-stacking direction. Charge separation was signalled by pronounced power-law photoluminescence decay polarized along the same axis. In the transverse direction, we observed exponential decay associated with excitons localized on individual monomers. We propose that this effect derives from an intrinsic directional charge-transfer interaction that can ultimately be programmed by molecular packing geometry.

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Change‐Point Localization and Wavelet Spectral Analysis of Single‐Molecule Time Series

Cited by 24 publications

References 104 publications

Competition between Bending and Internal Pressure Governs the Mechanics of Fluid Nanovesicles

Competition between Bending and Internal Pressure Governs the Mechanics of Fluid Nanovesicles

Simultaneous Real-Time Imaging of Leading and Lagging Strand Synthesis Reveals the Coordination Dynamics of Single Replisomes

Directional Charge Separation in Isolated Organic Semiconductor Crystalline Nanowires

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