Model-guided design of ligand-regulated RNAi for programmable control of gene expression

Progress in constructing biological networks will rely on the development of more advanced components that can be predictably modified to yield optimal system performance. We have engineered an RNA-based platform, which we call an shRNA switch, that provides for integrated ligand control of RNA interference (RNAi) by modular coupling of an aptamer, competing strand, and small hairpin (sh) RNA stem into a single component that links ligand concentration and target gene expression levels. A combined experimental and mathematical modelling approach identified multiple tuning strategies and moves towards a predictable framework for the forward design of shRNA switches. The utility of our platform is highlighted by the demonstration of fine-tuning, multi-input control, and model-guided design of shRNA switches with an optimized dynamic range. Thus, shRNA switches can serve as an advanced component for the construction of complex biological systems and offer a controlled means of activating RNAi in disease therapeutics

Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

Background: Microbial communities are involved in many processes relevant to industrial and medical biotechnology, such as the formation of biofilms, lignocellulosic degradation, and hydrogen production. The manipulation of synthetic and natural microbial communities and their underlying ecological parameters, such as fitness, evolvability, and variation, is an increasingly important area of research for synthetic biology. Results: Here, we explored how synthetic control of an endogenous circuit can be used to regulate a tradeoff between fitness in resource abundant and resource limited environments in a population of Saccharomyces cerevisiae. We found that noise in the expression of a key enzyme in ammonia assimilation, Gdh1p, mediated a tradeoff between growth in low nitrogen environments and stress resistance in high ammonia environments. We implemented synthetic control of an endogenous Gdh1p regulatory network to construct an engineered strain in which the fitness of the population was tunable in response to an exogenously-added small molecule across a range of ammonia environments. Conclusion: The ability to tune fitness and biological tradeoffs will be important components of future efforts to engineer microbial communities

Creating excitonic entanglement in quantum dots through the optical Stark effect

We show that two initially non-resonant quantum dots may be brought into resonance by the application of a single detuned laser. This allows for control of the inter-dot interactions and the generation of highly entangled excitonic states on the picosecond timescale. Along with arbitrary single qubit manipulations, this system would be sufficient for the demonstration of a prototype excitonic quantum computer.Comment: 4 pages, 3 figures; published version, figure 3 improved, corrections to RWA derive

Exciton lifetime in InAs/GaAs quantum dot molecules

The exciton lifetimes $T_1$ in arrays of InAs/GaAs vertically coupled quantum dot pairs have been measured by time-resolved photoluminescence. A considerable reduction of $T_1$ by up to a factor of $\sim$ 2 has been observed as compared to a quantum dots reference, reflecting the inter-dot coherence. Increase of the molecular coupling strength leads to a systematic decrease of $T_1$ with decreasing barrier width, as for wide barriers a fraction of structures shows reduced coupling while for narrow barriers all molecules appear to be well coupled. The coherent excitons in the molecules gain the oscillator strength of the excitons in the two separate quantum dots halving the exciton lifetime. This superradiance effect contributes to the previously observed increase of the homogeneous exciton linewidth, but is weaker than the reduction of $T_2$. This shows that as compared to the quantum dots reference pure dephasing becomes increasingly important for the molecules

Influence of the heterointerface sharpness on exciton recombination dynamics in an ensemble of (In,Al)As/AlAs quantum dots with indirect band-gap

The dynamics of exciton recombination in an ensemble of indirect band-gap (In,Al)As/AlAs quantum dots with type-I band alignment is studied. The lifetime of confined excitons which are indirect in momentum-space is mainly influenced by the sharpness of the heterointerface between the (In,Al)As quantum dot and the AlAs barrier matrix. Time-resolved photoluminescence experiments and theoretical model calculations reveal a strong dependence of the exciton lifetime on the thickness of the interface diffusion layer. The lifetime of excitons with a particular optical transition energy varies because this energy is obtained for quantum dots differing in size, shape and composition. The different exciton lifetimes, which result in photoluminescence with non-exponential decay obeying a power-law function, can be described by a phenomenological distribution function, which allows one to explain the photoluminescence decay with one fitting parameter only.Comment: 10 pages, 7 figure

Magnetic field control of photon echo in the electron-trion system: Shuffling of coherences between optically accessible and inaccessible states

We report on magnetic field induced oscillations of the photon echo signal from negatively charged excitons in a CdTe/(Cd,Mg)Te semiconductor quantum well. The oscillatory signal is due to Larmor precession of the electron spin about a transverse magnetic field and depends sensitively on the polarization configuration of the exciting and refocusing pulses. The echo amplitude can be fully tuned from maximum down to zero depending on the time delay between the two pulses and the magnetic field strength. The results are explained in terms of the optical Bloch equations accounting for the spin level structure of electron and trion.Comment: 8 pages, 2 figure

Optical control of coherent interactions between quantum dot electron spins

Coherent interactions between spins in quantum dots are a key requirement for quantum gates. We have performed pump-probe experiments in which pulsed lasers emitting at different photon energies manipulate two distinct subsets of electron spins within an inhomogeneous InGaAs quantum dot ensemble. The spin dynamics are monitored through their precession about an external magnetic field. These measurements demonstrate spin precession phase shifts and modulations of the magnitude of one subset of oriented spins after optical orientation of the second subset. The observations are consistent with results from a model using a Heisenberg-like interaction with microeV-strength.Comment: 5 pages, 4 figure