Absolute measurement of roughness and lateral-correlation length of random surfaces by use of the simplified model of image-speckle contrast

We present a method of image-speckle contrast for the nonprecalibration measurement of the root-mean-square roughness and the lateral-correlation length of random surfaces with Gaussian correlation. We use the simplified model of the speckle fields produced by the weak scattering object in the theoretical analysis. The explicit mathematical relation shows that the saturation value of the image-speckle contrast at a large aperture radius determines the roughness, while the variation of the contrast with the aperture radius determines the lateral-correlation length. In the experimental performance, we specially fabricate the random surface samples with Gaussian correlation. The square of the image-speckle contrast is measured versus the radius of the aperture in the 4f system, and the roughness and the lateral-correlation length are extracted by fitting the theoretical result to the experimental data. Comparison of the measurement with that by an atomic force microscope shows our method has a satisfying accuracy. (C) 2002 Optical Society of America.

Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

Interacting single atoms with nanophotonics for chip-integrated quantum networks

Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N >> 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N >> 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ~100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high controllability, with which we experimentally demonstrate a state-insensitive atom trap. We present initial investigations on nanophotonic crystal based structures as a platform for strong atom-photon interactions. The experimental advances and theoretical investigations carried out in this thesis provide a framework for and open the door to strong single atom-photon interactions using nanophotonics for chip-integrated quantum networks.

Mechanism study of femtosecond laser induced selective metallization (FLISM) on glass surfaces

We investigate the mechanism of selective metallization on glass surfaces with the assistance of femtosecond laser irradiation followed by electroless plating. Irradiation of femtosecond laser makes it possible to selectively deposit copper microstructures in the irradiated area on glass surfaces coated with silver nitrate films. The energy-dispersive X-ray (EDX) analyses reveal that silver atoms are produced on the surface of grooves formed by laser ablation, which serve as catalysis seeds for subsequent electroless copper plating. (C) 2008 Elsevier B.V. All rights reserved.

Vibrational pooling and constrained equilibration on surfaces

In this thesis, we provide a statistical theory for the vibrational pooling and fluorescence time dependence observed in infrared laser excitation of CO on an NaCl surface. The pooling is seen in experiment and in computer simulations. In the theory, we assume a rapid equilibration of the quanta in the substrate and minimize the free energy subject to the constraint at any time t of a fixed number of vibrational quanta N(t). At low incident intensity, the distribution is limited to one- quantum exchanges with the solid and so the Debye frequency of the solid plays a key role in limiting the range of this one-quantum domain. The resulting inverted vibrational equilibrium population depends only on fundamental parameters of the oscillator (ω_e and ω_eχ_e) and the surface (ω_D and T). Possible applications and relation to the Treanor gas phase treatment are discussed. Unlike the solid phase system, the gas phase system has no Debye-constraining maximum. We discuss the possible distributions for arbitrary N-conserving diatom-surface pairs, and include application to H:Si(111) as an example.

Computations are presented to describe and analyze the high levels of infrared laser-induced vibrational excitation of a monolayer of absorbed ¹³CO on a NaCl(100) surface. The calculations confirm that, for situations where the Debye frequency limited n domain restriction approximately holds, the vibrational state population deviates from a Boltzmann population linearly in n. Nonetheless, the full kinetic calculation is necessary to capture the result in detail.

We discuss the one-to-one relationship between N and γ and the examine the state space of the new distribution function for varied γ. We derive the Free Energy, F = NγkT − kTln(∑P_n), and effective chemical potential, μn ≈ γkT, for the vibrational pool. We also find the anti correlation of neighbor vibrations leads to an emergent correlation that appears to extend further than nearest neighbor.

Structure, chemistry, and energetics of organic and inorganic adsorbates on Ga-rich GaAs and GaP(001) surfaces

The work described in this dissertation includes fundamental investigations into three surface processes, namely inorganic film growth, water-induced oxidation, and organic functionalization/passivation, on the GaP and GaAs(001) surfaces. The techniques used to carry out this work include scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. Atomic structure, electronic structure, reaction mechanisms, and energetics related to these surface processes are discussed at atomic or molecular levels.

First, we investigate epitaxial Zn₃P₂ films grown on the Ga-rich GaAs(001)(6×6) surface. The film growth mechanism, electronic properties, and atomic structure of the Zn₃P₂/GaAs(001) system are discussed based on experimental and theoretical observations. We discover that a P-rich amorphous layer covers the crystalline Zn3P2 film during and after growth. We also propose more accurate picture of the GaP interfacial layer between Zn₃P₂ and GaAs, based on the atomic structure, chemical bonding, band diagram, and P-replacement energetics, than was previously anticipated.

Second, DFT calculations are carried out in order to understand water-induced oxidation mechanisms on the Ga-rich GaP(001)(2×4) surface. Structural and energetic information of every step in the gaseous water-induced GaP oxidation reactions are elucidated at the atomic level in great detail. We explore all reasonable ground states involved in most of the possible adsorption and decomposition pathways. We also investigate structures and energies of the transition states in the first hydrogen dissociation of a water molecule on the (2×4) surface.

Finally, adsorption structures and thermal decomposition reactions of 1-propanethiol on the Ga-rich GaP(001)(2×4) surface are investigated using high resolution STM, XPS, and DFT simulations. We elucidate adsorption locations and their associated atomic structures of a single 1-propanethiol molecule on the (2×4) surface as a function of annealing temperature. DFT calculations are carried out to optimize ground state structures and search transition states. XPS is used to investigate variations of the chemical bonding nature and coverage of the adsorbate species.

Coherent linking of periodic nano-ripples on a ZnO crystal surface induced by femtosecond laser pulses

We demonstrate the coherent linking of periodic nano-ripples formed on the surface of ZnO crystals induced by femtosecond laser pulses. By adjusting the distance between two laser scanning zones, the periodic nano-ripples induced by two separated laser writing processes can be coherently linked and the ZnO nanograting with much longer grooves is therefore produced. The length limitation of this kind of nanograting previously set by the laser focus size is thus overcome. The micro-Raman mapping technique is used to evaluate the quality of coherent linking, and the underlying physics is discussed. The demonstrated scheme is promising for producing large-size self-organized nanogratings induced by femtosecond laser pulses.

The autocorrelation of speckles in deep Fresnel diffraction region and characterizations of random self-affine fractal surfaces

This paper studies the correlation properties of the speckles in the deep Fresnel diffraction region produced by the scattering of rough self-affine fractal surfaces. The autocorrelation function of the speckle intensities is formulated by the combination of the light scattering theory of Kirchhoff approximation and the principles of speckle statistics. We propose a method for extracting the three surface parameters, i.e. the roughness w, the lateral correlation length xi and the roughness exponent alpha, from the autocorrelation functions of speckles. This method is verified by simulating the speckle intensities and calculating the speckle autocorrelation function. We also find the phenomenon that for rough surfaces with alpha = 1, the structure of the speckles resembles that of the surface heights, which results from the effect of the peak and the valley parts of the surface, acting as micro-lenses converging and diverging the light waves.