Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature

Simple way to correct the drift in surface-coupled optical tweezers using the laser reflection pattern

The surface-coupled optical tweezers are widely used to resolve small units of motion in biology. However, such motions could readily be interfered by the drift between the trap and surface. We present a simple and low-cost method to correct the drift both actively and passively based on video tracking the distance between the laser reflection pattern and the reference bead. As a result, we achieved sub-nanometer resolution and stability for the stuck bead over a broad range of averaging time (0.002-100 s) as demonstrated by the Allan deviation analysis. The sub-nanometer resolution was further manifested with step measurement. Finally, in double-stranded DNA and DNA hairpin stretching experiments, an extension resolution of 1-2 nm with the stability over 120 s has been demonstrated under a constant force. This work thus provides an easy way to bring the benefit of nanometer resolution and long-term stability to the surface-coupled optical tweezers.

Hybrid Systems for the Generation of Nonclassical Mechanical States via Quadratic Interactions

We present a method to implement two-phonon interactions between mechanical resonators and spin qubits in hybrid setups, and show that these systems can be applied for the generation of nonclassical mechanical states even in the presence of dissipation. In particular, we demonstrate that the implementation of a two-phonon Jaynes-Cummings Hamiltonian under coherent driving of the qubit yields a dissipative phase transition with similarities to the one predicted in the model of the degenerate parametric oscillator: beyond a certain threshold in the driving amplitude, the driven-dissipative system sustains a mixed steady state consisting of a "jumping cat," i.e., a cat state undergoing random jumps between two phases. We consider realistic setups and show that, in samples within reach of current technology, the system features nonclassical transient states, characterized by a negative Wigner function, that persist during timescales of fractions of a second.

Method for high frequency tracking and sub-nm sample stabilization in single molecule fluorescence microscopy

While fluorescence microscopes and atomic force microscopes are widely used to visualize, track, and manipulate single biomolecules, the resolution of these methods is limited by sample drift. To minimize drift, active feedback methods have recently been used to stabilize single molecule microscopes on the sub-nanometer scale. However, these methods require high intensity lasers which limits their application in single molecule fluorescence measurements. Furthermore, these feedback methods do not track user-defined regions of the sample, but rather monitor the relative displacement of an unknown point on a fiducial marker, which limits their use in biological force measurements. To overcome these limitations, we have developed a novel method to image, track and stabilize a sample using low laser intensities. We demonstrate the capabilities of our approach by tracking a user-chosen point on a fiducial marker at 8.6 kHz and stabilizing it with sub-nanometer resolution. We further showcase the application of our method in single molecule fluorescence microscopy by imaging and stabilizing individual fluorescently-tagged streptavidin proteins under biologically relevant conditions. We anticipate that our method can be easily used to improve the resolution of a wide range of single molecule fluorescence microscopy and integrated force-fluorescence applications.

Label-Free Single-Molecule Imaging with Numerical-Aperture-Shaped Interferometric Scattering Microscopy

Our ability to optically interrogate nanoscopic objects is controlled by the difference between their extinction cross sections and the diffraction-limited area to which light can be confined in the far field. We show that a partially transmissive spatial mask placed near the back focal plane of a high numerical aperture microscope objective enhances the extinction contrast of a scatterer near an interface by approximately T^-1/2, where T is the transmissivity of the mask. Numerical-aperture-based differentiation of background from scattered light represents a general approach to increasing extinction contrast and enables routine label-free imaging down to the single-molecule level.

A Surface-Coupled Optical Trap with 1-bp Precision via Active Stabilization

Optical traps can measure bead motions with Å-scale precision. However, using this level of precision to infer 1-bp motion of molecular motors along DNA is difficult, since a variety of noise sources degrade instrumental stability. In this chapter, we detail how to improve instrumental stability by (1) minimizing laser pointing, mode, polarization, and intensity noise using an acousto-optical-modulator mediated feedback loop and (2) minimizing sample motion relative to the optical trap using a three-axis piezo-electric-stage mediated feedback loop. These active techniques play a critical role in achieving a surface stability of 1 Å in 3D over tens of seconds and a 1-bp stability and precision in a surface-coupled optical trap over a broad bandwidth (Δf = 0.03-2 Hz) at low force (6 pN). These active stabilization techniques can also aid other biophysical assays that would benefit from improved laser stability and/or Å-scale sample stability, such as atomic force microscopy and super-resolution imaging.

Implementation and Tuning of an Optical Tweezers Force-Clamp Feedback System

Feedback systems can be used to control the value of a system variable. In optical tweezers, active feedback is often implemented to either keep the position or tension applied to a single biomolecule constant. Here, we describe the implementation of the latter: an optical force-clamp setup that can be used to study the motion of processive molecular motors under a constant load. We describe the basics of a software-implemented proportional-integral-derivative (PID) controller, how to tune it, and how to determine its optimal feedback rate. Limitations, possible feed-forward applications, and extensions into two- and three-dimensional optical force clamps are discussed. The feedback is ultimately limited by thermal fluctuations and the compliance of the involved molecules. To investigate a particular mechanical process, understanding the basics and limitations of the feedback system will be helpful for choosing the proper feedback hardware, for optimizing the system parameters, and for the design of the experiment.

-1 Programmed Ribosomal Frameshifting as a Force-Dependent Process

-1 Programmed ribosomal frameshifting is a translational recoding event in which ribosomes slip backward along messenger RNA presumably due to increased tension disrupting the codon-anticodon interaction at the ribosome's coding site. Single-molecule physical methods and recent experiments characterizing the physical properties of mRNA's slippery sequence as well as the mechanical stability of downstream mRNA structure motifs that give rise to frameshifting are discussed. Progress in technology, experimental assays, and data analysis methods hold promise for accurate physical modeling and quantitative understanding of -1 programmed ribosomal frameshifting.