The Feedback Capacity of the Binary Erasure Channel With a No-Consecutive-Ones Input Constraint

The input-constrained erasure channel with feedback is considered, where the binary input sequence contains no consecutive ones, i.e., it satisfies the (1, infinity)-RLL constraint. We derive the capacity for this setting, which can be expressed as C-is an element of = max(0 <= p <= 0.5) (1-is an element of) H-b (p)/1+(1-is an element of) p, where is an element of is the erasure probability and Hb(.) is the binary entropy function. Moreover, we prove that a priori knowledge of the erasure at the encoder does not increase the feedback capacity. The feedback capacity was calculated using an equivalent dynamic programming (DP) formulation with an optimal average-reward that is equal to the capacity. Furthermore, we obtained an optimal encoding procedure from the solution of the DP, leading to a capacity-achieving, zero-error coding scheme for our setting. DP is, thus, shown to be a tool not only for solving optimization problems, such as capacity calculation, but also for constructing optimal coding schemes. The derived capacity expression also serves as the only non-trivial upper bound known on the capacity of the input-constrained erasure channel without feedback, a problem that is still open.

Optimal Guidance for Accurate Lunar Soft Landing with Minimum Fuel Consumption using Model Predictive Static Programming

In this paper the soft lunar landing with minimum fuel expenditure is formulated as a nonlinear optimal guidance problem. The realization of pinpoint soft landing with terminal velocity and position constraints is achieved using Model Predictive Static Programming (MPSP). The high accuracy of the terminal conditions is ensured as the formulation of the MPSP inherently poses final conditions as a set of hard constraints. The computational efficiency and fast convergence make the MPSP preferable for fixed final time onboard optimal guidance algorithm. It has also been observed that the minimum fuel requirement strongly depends on the choice of the final time (a critical point that is not given due importance in many literature). Hence, to optimally select the final time, a neural network is used to learn the mapping between various initial conditions in the domain of interest and the corresponding optimal flight time. To generate the training data set, the optimal final time is computed offline using a gradient based optimization technique. The effectiveness of the proposed method is demonstrated with rigorous simulation results.

Evolution induced catastrophe in a nonlinear dynamical model of material failure

In order to study the failure of disordered materials, the ensemble evolution of a nonlinear chain model was examined by using a stochastic slice sampling method. The following results were obtained. (1) Sample-specific behavior, i.e. evolutions are different from sample to sample in some cases under the same macroscopic conditions, is observed for various load-sharing rules except in the globally mean field theory. The evolution according to the cluster load-sharing rule, which reflects the interaction between broken clusters, cannot be predicted by a simple criterion from the initial damage pattern and even then is most complicated. (2) A binary failure probability, its transitional region, where globally stable (GS) modes and evolution-induced catastrophic (EIC) modes coexist, and the corresponding scaling laws are fundamental to the failure. There is a sensitive zone in the vicinity of the boundary between the GS and EIC regions in phase space, where a slight stochastic increment in damage can trigger a radical transition from GS to EIC. (3) The distribution of strength is obtained from the binary failure probability. This, like sample-specificity, originates from a trans-scale sensitivity linking meso-scopic and macroscopic phenomena. (4) Strong fluctuations in stress distribution different from that of GS modes may be assumed as a precursor of evolution-induced catastrophe (EIC).

An Efficient Front-Tracking Method For Fully Nonlinear Interfacial Waves

A fully nonlinear and dispersive model within the framework of potential theory is developed for interfacial (2-layer) waves. To circumvent the difficulties arisen from the moving boundary problem a viable technique based on the mixed Eulerian and Lagrangian concept is proposed: the computing area is partitioned by a moving mesh system which adjusts its location vertically to conform to the shape of the moving boundaries but keeps frozen in the horizontal direction. Accordingly, a modified dynamic condition is required to properly compute the boundary potentials. To demonstrate the effectiveness of the current method, two important problems for the interfacial wave dynamics, the generation and evolution processes, are investigated. Firstly, analytical solutions for the interfacial wave generations by the interaction between the barotropic tide and topography are derived and compared favorably with the numerical results. Furthermore simulations are performed for the nonlinear interfacial wave evolutions at various water depth ratios and satisfactory agreement is achieved with the existing asymptotical theories. (c) 2008 Elsevier Inc. All rights reserved.

Scenario Cluster Lagrangian Decomposition in two stage stochastic mixed 0-1 optimization

In this paper we introduce four scenario Cluster based Lagrangian Decomposition (CLD) procedures for obtaining strong lower bounds to the (optimal) solution value of two-stage stochastic mixed 0-1 problems. At each iteration of the Lagrangian based procedures, the traditional aim consists of obtaining the solution value of the corresponding Lagrangian dual via solving scenario submodels once the nonanticipativity constraints have been dualized. Instead of considering a splitting variable representation over the set of scenarios, we propose to decompose the model into a set of scenario clusters. We compare the computational performance of the four Lagrange multiplier updating procedures, namely the Subgradient Method, the Volume Algorithm, the Progressive Hedging Algorithm and the Dynamic Constrained Cutting Plane scheme for different numbers of scenario clusters and different dimensions of the original problem. Our computational experience shows that the CLD bound and its computational effort depend on the number of scenario clusters to consider. In any case, our results show that the CLD procedures outperform the traditional LD scheme for single scenarios both in the quality of the bounds and computational effort. All the procedures have been implemented in a C++ experimental code. A broad computational experience is reported on a test of randomly generated instances by using the MIP solvers COIN-OR and CPLEX for the auxiliary mixed 0-1 cluster submodels, this last solver within the open source engine COIN-OR. We also give computational evidence of the model tightening effect that the preprocessing techniques, cut generation and appending and parallel computing tools have in stochastic integer optimization. Finally, we have observed that the plain use of both solvers does not provide the optimal solution of the instances included in the testbed with which we have experimented but for two toy instances in affordable elapsed time. On the other hand the proposed procedures provide strong lower bounds (or the same solution value) in a considerably shorter elapsed time for the quasi-optimal solution obtained by other means for the original stochastic problem.

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.

On Ultrafast Time-Domain TeraHertz Spectroscopy in the Condensed Phase: Linear Spectroscopic Measurements of Hydrogen-Bond Dynamics of Astrochemical Ice Analogs and Nonlinear TeraHertz Kerr Effect Measurements of Vibrational Quantum Beats

Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz (THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz, 3 cm^-1 to 300 cm^-1, or 3000 μm to 30 μm) has been shown to provide unique possibilities in the study of condensed-phase processes. The goal of this work is to expand the possibilities available in the THz region and undertake new investigations of fundamental interest to chemistry. Since we are fundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz spectroscopy can provide new understanding: astrochemistry and solvation science. To advance these fields, we had to develop new instrumentation that would enable the experiments necessary to answer new questions in either astrochemistry or solvation science. We first developed a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz (THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm^-1) and the mid-IR (400 - 4000 cm^-1). The importance of astrochemical ices lies in their key role in the formation of complex organic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of performing variety of spectroscopic studies that can provide especially relevant laboratory data to support astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric Observatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array (ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm plasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz (~0.3 cm^-1) resolution.

Using the above instrumentation, experimental spectra of astrochemical ice analogs of water and carbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high vacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a new feature in both amorphous solid water and crystalline water at 33 cm^-1 (1 THz). In addition, our studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide as it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz spectra of mixed and layered ices are further analyzed by fitting their spectra features to those of pure amorphous solid water and crystalline water ice to quantify the effects of temperature changes on structure. From the results of this work, it appears that THz spectroscopy is potentially well suited to study thermal transformations within the ice.

To advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear THz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy. We implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased THz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS), and high numerical aperture optics which generates THz electric field in excess of 300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz (THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar interaction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument improves on both the frequency coverage, and sensitivity previously reported; it also ensures a backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we observe a quantum beat at 3.66 THz (122 cm^-1), in exact agreement with the fundamental transition frequency of the υ4 vibration of the molecule. This result provides new insight into dipolar vs. Raman selection rules at terahertz frequencies.

To conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab. We report the first results from an experiment using a plasma-based THz source for nonlinear spectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal resolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping. Finally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz data and how such a scheme could be implemented in the Blake lab. The instruments developed herein will hopefully remain a part of the groups core competencies and serve as building blocks for the next generation of THz instrumentation that pushes the frontiers of both chemistry and the scientific enterprise as a whole.

Coincidence point theorems in quasi-metric spaces without assuming the mixed monotone property and consequences in G-metric spaces

In this paper, we present some coincidence point theorems in the setting of quasi-metric spaces that can be applied to operators which not necessarily have the mixed monotone property. As a consequence, we particularize our results to the field of metric spaces, partially ordered metric spaces and G-metric spaces, obtaining some very recent results. Finally, we show how to use our main theorems to obtain coupled, tripled, quadrupled and multidimensional coincidence point results.

A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations

Finding an appropriate turbulence model for a given flow case usually calls for extensive experimentation with both models and numerical solution methods. This work presents the design and implementation of a flexible, programmable software framework for assisting with numerical experiments in computational turbulence. The framework targets Reynolds-averaged Navier-Stokes models, discretized by finite element methods. The novel implementation makes use of Python and the FEniCS package, the combination of which leads to compact and reusable code, where model- and solver-specific code resemble closely the mathematical formulation of equations and algorithms. The presented ideas and programming techniques are also applicable to other fields that involve systems of nonlinear partial differential equations. We demonstrate the framework in two applications and investigate the impact of various linearizations on the convergence properties of nonlinear solvers for a Reynolds-averaged Navier-Stokes model. © 2011 Elsevier Ltd.

Linear and nonlinear model large-eddy simulations of a plane jet

The nonlinear Kosovic, and mixed Leray and α subgrid scale models are contrasted with linear Smagorinsky and Yoshizawa Large Eddy Simulations for a Re = 4000 plane jet simulation. Comparisons are made with Direct Numerical Simulation data and measurements. Global properties of the jet such as the spreading and centreline velocity decay rates are investigated. The mean-flow and turbulence parameters in the self-similar region are also studied. All models generally give encouraging agreement with the Direct Numerical Simulation data and reliable measurements. Solution differences for the models are relatively minor, none giving clear improvements for all data comparisons.

A 1,000 Frames/s Programmable Vision Chip with Variable Resolution and Row-Pixel-Mixed Parallel Image Processors

A programmable vision chip with variable resolution and row-pixel-mixed parallel image processors is presented. The chip consists of a CMOS sensor array, with row-parallel 6-bit Algorithmic ADCs, row-parallel gray-scale image processors, pixel-parallel SIMD Processing Element (PE) array, and instruction controller. The resolution of the image in the chip is variable: high resolution for a focused area and low resolution for general view. It implements gray-scale and binary mathematical morphology algorithms in series to carry out low-level and mid-level image processing and sends out features of the image for various applications. It can perform image processing at over 1,000 frames/s (fps). A prototype chip with 64 x 64 pixels resolution and 6-bit gray-scale image is fabricated in 0.18 mu m Standard CMOS process. The area size of chip is 1.5 mm x 3.5 mm. Each pixel size is 9.5 mu m x 9.5 mu m and each processing element size is 23 mu m x 29 mu m. The experiment results demonstrate that the chip can perform low-level and mid-level image processing and it can be applied in the real-time vision applications, such as high speed target tracking.

Multiphoton ionization of pyrrole-water mixed clusters

Multiphoton ionization of the hydrogen,bonded pyrrole-water clusters (C4H5N)(n)(H2O)(m) is studied with a reflectron-time of flight mass spectrometer at 355 mn. With increasing partial concentration of pyrrole in a gas mixture source, a series of poly-pyrrole-water binary-mixed cluster ions can be observed, including unprotonated cluster ions [(C4H5N)(x)(H2O)(y)](+), protonated cluster ions [(C4H5N)(x)(H2O)(y)](+) and dehydrogenated cluster ions [(C4H4N)(C4H5N)(x)(H2O)(y)](+). Ab initio calculations of their structures, bond strengths, charge distributions and reaction energies are carried out. Stable structures of these clusters are obtained from the calculations. A probable formation mechanism of the cluster ions [(C4H5N)(x)(H2O)(y)](+), [(C4H5N)(x)(H2O)(y)]H+ and [(C4H4N)(C4H5N)(x) (H2O)(y)](+) is supposed to be the ionization of clusters followed by dissociation.

Microphase Separation of Mixed Polymer Brushes: Dependence of the Morphology on Grafting Density, Composition, Chain-Length Asymmetry, Solvent Quality, and Selectivity

Microphase separation of binary mixed A/B polymer brushes exposed to different solvents is studied using Single-Chain-in-Mean-Field simulations. Effects of solvent quality and selectivity, grafting density, composition, and chain-length asymmetry are systematically investigated, and diagrams of morphologies in various solvents are constructed as a function of grafting density and composition or chain-length asymmetry. The structure of the microphase segregated morphologies lacks long-range periodic order, and it is analyzed quantitatively Using Minkowski measures.

pH-potentiometric study on rare earths and calcium binary and ternary complexes with DL-malic acid and L-hydroxyproline

The stability constants of M-L binary system and M-L-L' (M = La3+ similar to Yb3+, Y3+ and Ca2+; L= DL-malic aicd, L' = L-hydroxyproline) ternary system were determined by pH-(0)-tentiometric method under the simulating physiological condition(37 degrees C, I=0.15 mol/L NaCl). The complex species MpLqLr'H-s(abbr as pqrs) in the sytems were ascertained by program COMPLEX. The results show that there are three species(1101, 1100 and 1200) in M-L binary system and one species(1010) in M-L' binary system. In addition to the above four species, a new species, 1112 was found in the M-L-L' ternary system, which is the only species of mixed ligands. Rare earth ions form more stable complexes than calcium ion does and the stability differences between their complexes in the ternary system are less than that in the binary system. The distributions of all the species in La-L-L' ternary system vs pH are discussed.

Study on binary system comprising a non-mesogen and a mesogen

Mixed liquid crystal formation has been studied in a new binary system comprising paranitroazobenzene derivatives, in which one component was a mesogen and the other was a non-mesogen. The mixtures were found to exhibit a monotropic nematic phase which was converted to an enantiotropic phase in specific ranges of temperature and concentration. The latent liquid crystal-isotropic transition temperature (LTP) of the non-mesogen was obtained by using the extrapolation method of the transition temperature-composition curve and the equal-G analysis method. The LTPs of the non-mesogen obtained by the above two methods showed good agreement with each other. The low-temperature transition of the mixtures detected by DSC was attributed to a change of the crystallite size.