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Qiao Lu

Publications and source records attributed to Qiao Lu.

3 recordsLinked to original sources

Observation of periodic optical spectra and soliton molecules in a novel passively mode-locked fiber laser

Due to the necessity of making a series of random adjustments after mode-locking in most experiments for preparing soliton molecules, the repeatability of the preparations remains a challenge. Here, we introduce a novel all-polarization-maintaining erbium-doped fiber laser that utilizes a nonlinear amplifying loop mirror for mode-locking and features a linear shape. This laser can stably output soliton molecules without any additional adjustment once the mode-locking self-starts. Moreover, it can achieve the transition from soliton molecule state to soliton state, and then to multi-pulse state by reducing the pumping power. The unconventional method of generating multi-pulses, combined with a wide pumping power range of 200--640 mW for maintaining mode-locking, allowed us to observe periodic optical spectra with two complete cycles for the first time. Based on the experimental facts, we develop a multistability model to explain this phenomenon. With its ability to switch between three stable states, this flexible laser can serve as a versatile toolbox for studying soliton dynamics.

physics.optics

Target search in the CRISPR/Cas9 system: Facilitated diffusion with target cues

We study how Cas9, a central component of the CRISPR/Cas9 system, searches for a target sequence on the DNA. We propose a model that includes as key ingredients 3D diffusion, 1D sliding along the DNA, and the effect of short binding sequences preceding the target (protospacer adjacent sequences -- PAMs). This latter aspect constitutes the main difference with traditional facilitated diffusion of transcription factors. We solve our model, obtaining an expression for the average search time of Cas9 for its target. We find that experimentally measured kinetic parameters are close to the values yielding an optimal search time. Our results rationalize the role of PAMs in guiding the search process, and show that Cas9 searches for its targets in a nearly optimal way.

q-bio.SC

Search and localization dynamics of the CRISPR/Cas9 system

The CRISPR/Cas9 system acts as the prokaryotic immune system and has important applications in gene editing. The protein Cas9 is one of its crucial components. The role of Cas9 is to search for specific target sequences on the DNA and cleave them. In this Letter, we introduce a model of facilitated diffusion for Cas9 and fit its parameters to single-molecule experiments. Our model confirms that Cas9 search for targets by sliding, but shows that its sliding length is rather short. We then investigate how Cas9 explores a long stretch of DNA containing randomly placed targets. We solve this problem by mapping it into the theory of Anderson localization in condensed matter physics. Our theoretical approach rationalizes experimental evidences on the distribution of Cas9 molecules along the DNA.

q-bio.SC