We perform single-molecule partitioning measurements of the free energy of chain confinement and selfexclusion as a function of confinement dimension and buffer ionic strength via single-molecule Tetris. Individual DNA chains, confined in a nanoslit with a lattice of embedded nanocavities, partition their contour between the cavities. Changes in device geometry and buffer chemistry lead to changes in the number of cavities occupied. We are able to deduce the confinement free energy difference between the nanocavities and the nanoslit by observing how the number of cavities occupied by a single chain varies as a function of device dimension. These measurements enable us to confirm theoretical predictions for confinement free energy based on worm-like chain formalism and quantify the chain effective width w, providing a direct measure of the size of excluded-volume effect on a single-chain level.
Here we explore thermally driven contour fluctuations within a single DNA chain partitioned between two embedded cavity reservoirs in a nanofluidic slit. Analysis of integrated cavity intensity suggests that contour is exchanged dynamically between the reservoirs via modes that resemble the symmetric and antisymmetric modes of a coupled harmonic oscillator. The relaxation time of the modes is measured as a function of cavity width and spacing. Langevin dynamics simulations reproduce our observations and motivate a free energy model with a blob-type hydrodynamic friction, developed and used to deduce how the measured relaxation times for the modes depend on device parameters. The relaxation time of the antisymmetric mode was found to be consistent with an excluded volume-based stiffness while the faster symmetric mode depends on additional entropic and elastic parameters. ■ INTRODUCTIONThe study of the static properties of DNA in model nanofluidic geometries such as nanoslits and nanochannels has revealed how static polymer conformation depends on device dimension. 1 In contrast to nanoslit and nanochannel geometries that have only a single degree of freedom, i.e., the vertical height of the slit or width of the channel, complex nanofluidic environments contain regions of varying dimension and confinement scale. These multiple degrees of freedom can be tuned in order to control the static and dynamic molecular properties of single molecules. 2 In addition, complex environments lead to new properties such as single chain trapping at locally open sites in the structure and partitioning of contour between multiple trapping sites. Natural sieving media such as gels are examples of complex nanofluidic environments as are micro/nanofabricated entropic trapping arrays 3 and the zeromode waveguide structures 4 used in some next-generation sequencing technologies.Of particular interest are the time scales of internal fluctuations of contour. For biotechnologies utilizing nanoconfinement to study DNA, it is necessary to understand internal fluctuations, to ensure that independent samples are being imaged, and to minimize noise or maximize accessible imaging time. Initial measurements by Reisner et al. of DNA relaxation times in nanochannels showed a relaxation time scale on the order of a second, with a local maximum at a transition between two regimes near the Kuhn length. 5 In slits, measurements of diffusion and relaxation time by Hsieh et al. show dynamics in between those described by Rouse and Zimm physics. 6 In a more detailed study, structural time correlations in slit-confined DNA were examined by Jones et al., who found that the hydrodynamic exponent of internal correlations grew with spatial separation toward a plateau governed by Zimm physics, before decaying as the separation exceeded the size of the channel, providing experimental evidence that hydrodynamic interactions are screened beyond length scales equivalent to the height of the slit. The internal fluctuation modes of nanoconfined DNA were examined by Ka...
We analyze a modified Bose-Hubbard model, where two cavities having on-site Kerr interactions are subject to two-photon driving and correlated dissipation. We derive an exact solution for the steady state of this interacting drivendissipative system, and use it show that the system permits the preparation and stabilization of pure entangled non-Gaussian states, so-called entangled cat states. Unlike previous proposals for dissipative stabilization of such states, our approach requires only a linear coupling to a single engineered reservoir (as opposed to nonlinear couplings to two or more reservoirs). Our scheme is within the reach of state-of-the-art experiments in circuit QED.
Measurement-based quantum computation, an alternative paradigm for quantum information processing, uses simple measurements on qubits prepared in cluster states, a class of multiparty entangled states with useful properties. Here we propose and analyze a scheme that takes advantage of the interplay between spin-orbit coupling and superexchange interactions, in the presence of a coherent drive, to deterministically generate macroscopic arrays of cluster states in fermionic alkaline earth atoms trapped in three dimensional (3D) optical lattices. The scheme dynamically generates cluster states without the need of engineered transport, and is robust in the presence of holes, a typical imperfection in cold atom Mott insulators. The protocol is of particular relevance for the new generation of 3D optical lattice clocks with coherence times > 10 s, two orders of magnitude larger than the cluster state generation time. We propose the use of collective measurements and time-reversal of the Hamiltonian to benchmark the underlying Ising model dynamics and the generated many-body correlations. arXiv:1812.07686v2 [quant-ph]
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