The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently, optical sensors have been shown to allow noninvasive time-resolved measurements of the dynamic polarizability of single-molecules. Here we introduce a method to efficiently predict the dynamic polarizability from the atomic configuration of a given macromolecule. This provides a means to connect the measured dynamic polarizability to the underlying structure of the molecule, and therefore to connect temporal measurements to structural dynamics. To illustrate the methodology we calculate the change in polarizability as a function of time based on conformations extracted from molecular dynamics simulations and using different conformations of motor proteins solved crystalographically. This allows us to quantify the magnitude of the changes in polarizablity due to thermal and functional motions.

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Label-free biosensors are important tools for clinical diagnostics and for studying biology at the single molecule level. The development of optical label-free sensors has allowed extreme sensitivity, but can expose the biological sample to photodamage. Moreover, the fragility and complexity of these sensors can be prohibitive to applications. To overcome these problems, we develop a quantum noise limited exposed-core fiber sensor providing robust platform for label-free biosensing with a natural path toward microfluidic integration. We demonstrate the detection of single nanoparticles down to 25 nm in radius with optical intensities beneath known biophysical damage thresholds.

After advent of graphene as a saturable absorber many experiments have been conducted to produce short pulse duration pulses. Here, we have measured the properties of flake-graphene saturable absorber mirrors of various flake sizes dependent on fabrication technique. These mirrors enabled us to obtain a large mode-locking bandwidth of 16nm in an erbium-doped fiber laser. Mirrors with large flake size and multi-layered thickness induce strong pulse shaping and reflect modelocked train of pulses with very large bandwidths.