Assessing base-resolution DNA mechanics on the genome scale.

Intrinsic DNA properties including bending play a crucial role in diverse biological systems. A recent advance in a high-throughput technology called loop-seq makes it possible to determine the bendability of hundred thousand 50-bp DNA duplexes in one experiment. However, it's still challenging to assess base-resolution sequence bendability in large genomes such as human, which requires thousands of such experiments. Here, we introduce 'BendNet'-a deep neural network to predict the intrinsic DNA bending at base-resolution by using loop-seq results in yeast as training data. BendNet can predict the DNA bendability of any given sequence from different species with high accuracy. To explore the utility of BendNet, we applied it to the human genome and observed DNA bendability is associated with chromatin features and disease risk regions involving transcription/enhancer regulation, DNA replication, transcription factor binding and extrachromosomal circular DNA generation. These findings expand our understanding on DNA mechanics and its association with transcription regulation in mammals. Lastly, we built a comprehensive resource of genomic DNA bendability profiles for 307 species by applying BendNet, and provided an online tool to assess the bendability of user-specified DNA sequences (http://www.dnabendnet.com/).

Conservation-Law-Based Global Bounds to Quantum Optimal Control.

Active control of quantum systems enables diverse applications ranging from quantum computation to manipulation of molecular processes. Maximum speeds and related bounds have been identified from uncertainty principles and related inequalities, but such bounds utilize only coarse system information and loosen significantly in the presence of constraints and complex interaction dynamics. We show that an integral-equation-based formulation of conservation laws in quantum dynamics leads to a systematic framework for identifying fundamental limits to any quantum control scenario. We demonstrate the utility of our bounds in three scenarios-three-level driving, decoherence suppression, and maximum-fidelity gate implementations-and show that in each case our bounds are tight or nearly so. Global bounds complement local-optimization-based designs, illuminating performance levels that may be possible, as well as those that cannot be surpassed.

Computational Bounds to Light-Matter Interactions via Local Conservation Laws.

We develop a computational framework for identifying bounds to light-matter interactions, originating from polarization-current-based formulations of local conservation laws embedded in Maxwell's equations. We propose an iterative method for imposing only the maximally violated constraints, enabling rapid convergence to global bounds. Our framework can identify bounds to the minimum size of any scatterer that encodes a specific linear operator, given only its material properties, as we demonstrate for the optical computation of a discrete Fourier transform. It further resolves bounds on far-field scattering properties over any arbitrary bandwidth, where previous bounds diverge.

Examining second-harmonic generation of high-order Laguerre-Gaussian modes through a single cylindrical lens.

We experimentally investigate the second-harmonic generation of a high-order Laguerre-Gaussian (LG) mode under the quasi-phase-matching (QPM) configuration. First, we introduce a simple method to observe the azimuthal (l) and radial (p) indices of the high-order LG modes. Based on the astigmatic transformation technique, l and p are revealed in the number of dark stripes of the converted pattern in the focal plane. Then, using this efficient method of measurement, we demonstrate in experiments a second-harmonic LG mode with its radial and azimuthal indices being twice those of the inputted fundamental wave through QPM in a periodically poled KTP crystal. Our results provide a feasible way to obtain simultaneously the LG modes with larger radial and azimuthal indices.

On-chip generation of broadband high-order Laguerre-Gaussian modes in a metasurface.

With experimental results, we demonstrate the generation of high-order Laguerre-Gaussian modes with non-zero radial indices using a metal meta-surface, which is composed of a series of rectangle nanoholes with different orientation angles. The phase shift after transmission through the metasurface is determined by the orientation angle of the nanohole. This device works over a broad wavelength band ranging from 700 to 1000 nm. Moreover, we achieve a LG mode with a radial mode index of 10. Our results provide an integrated method to obtain high-order LG modes, which can be used to enhance the capacity in optical communication and manipulation.

Broadband Variable Meta-Axicons Based on Nano-Aperture Arrays in a Metallic Film.

Metasurfaces are two-dimensional metamaterials composed of a carefully designed series of subwavelength meta-atom (antenna or aperture) arrays. These surfaces can manipulate the phase, amplitude and polarization of output light by changing the shapes and orientations of the meta-atoms on a subwavelength scale. Using these properties, we experimentally demonstrate variable meta-axicons composed of rectangular nano-apertures arranged in several concentric rings that can focus left circularly polarized (LCP) light into a real Bessel beam and defocus right circular polarized (RCP) light to form a virtual beam. A desired phase discontinuity in cross-polarized transmitted light is introduced along the interface by controlling the orientations of the nano-apertures. In addition, the meta-axicons can generate Bessel beams of arbitrary orders by suitable design of the phase profile along the surface. The meta-axicons demonstrate broadband optical properties that can switch the wavelength of the incident light from 690 nm to 1050 nm. These variable meta-axicons open a path towards the development of new applications using integrated beam shaping devices.

Next Generation of Phonon Tests of Lorentz Invariance Using Quartz BAW Resonators.

We demonstrate technological improvements in phonon sector tests of the Lorentz invariance that implement quartz bulk acoustic wave oscillators. In this experiment, room temperature oscillators with state-of-the-art phase noise are continuously compared on a platform that rotates at a rate of order of a cycle per second. The discussion is focused on improvements in noise measurement techniques, data acquisition, and data processing. Preliminary results of the second generation of such tests are given, and indicate that standard model extension coefficients in the matter sector can be measured at a precision of order 10-16 GeV after taking a year's worth of data. This is equivalent to an improvement of two orders of magnitude over the prior acoustic phonon sector experiment.

Electrochromic-Tuned Plasmonics for Photothermal Sterile Window.

Electrochromic materials are widely used in smart windows. An ideal future electrochromic window would be able to control visible light transmission, tune building's heat conversion of near-infrared (NIR) solar radiation, and reduce attacks by microorganisms. To date, most of the reports have primarily focused on visible-light transmission modulation using electrochromic materials. Herein, we report the fabrication of an electrochromic-photothermal film by integrating electrochromic WO3 with plasmonic Au nanostructures and demonstrate its adjustability during optical transmission and photothermal conversion of visible and NIR lights. The localized surface plasmon resonance (LSPR) of Au nanostructures and the broadband nonradiative plasmon decay are proposed to be tunable using both the electric field and the WO3 substrate. Further enhanced photothermal conversion is achieved in colored state, which is attributed to coupling of traditional visible-band optical switching with NIR-LSPR extinction. The resulted electrochromic-photothermal film can also effectively reduce the numbers of attacking microorganisms, thus promising for use as a sterile smart window for advanced applications.