Wave algorithms:Optimal database search and catalysis

Grover's database search algorithm, although discovered in the context of quantum computation, can be implemented using any physical system that allows superposition of states. A physical realization of this algorithm is described using coupled simple harmonic oscillators, which can be exactly solved in both classical and quantum domains. Classical wave algorithms are far more stable against decoherence compared to their quantum counterparts. In addition to providing convenient demonstration models, they may have a role in practical situations, such as catalysis.

Control of a Duct Flow Network for Wind Display in a Virtual Environment

Control of flow in duct networks has a myriad of applications ranging from heating, ventilation, and air-conditioning to blood flow networks. The system considered here provides vent velocity inputs to a novel 3-D wind display device called the TreadPort Active Wind Tunnel. An error-based robust decentralized sliding-mode control method with nominal feedforward terms is developed for individual ducts while considering cross coupling between ducts and model uncertainty as external disturbances in the output. This approach is important due to limited measurements, geometric complexities, and turbulent flow conditions. Methods for resolving challenges such as turbulence, electrical noise, valve actuator design, and sensor placement are presented. The efficacy of the controller and the importance of feedforward terms are demonstrated with simulations based upon an experimentally validated lumped parameter model and experiments on the physical system. Results show significant improvement over traditional control methods and validate prior assertions regarding the importance of decentralized control in practice.

Context aware M-commerce services: C-IOB model approach

Context-aware computing is useful in providing individualized services focusing mainly on acquiring surrounding context of user. By comparison, only very little research has been completed in integrating context from different environments, despite of its usefulness in diverse applications such as healthcare, M-commerce and tourist guide applications. In particular, one of the most important criteria in providing personalized service in a highly dynamic environment and constantly changing user environment, is to develop a context model which aggregates context from different domains to infer context of an entity at the more abstract level. Hence, the purpose of this paper is to propose a context model based on cognitive aspects to relate contextual information that better captures the observation of certain worlds of interest for a more sophisticated context-aware service. We developed a C-IOB (Context-Information, Observation, Belief) conceptual model to analyze the context data from physical, system, application, and social domains to infer context at the more abstract level. The beliefs developed about an entity (person, place, things) are primitive in most theories of decision making so that applications can use these beliefs in addition to history of transaction for providing intelligent service. We enhance our proposed context model by further classifying context information into three categories: a well-defined, a qualitative and credible context information to make the system more realistic towards real world implementation. The proposed model is deployed to assist a M-commerce application. The simulation results show that the service selection and service delivery of the system are high compared to traditional system.

Instability Analysis of Nonlinear Surface Waves in a Circular Cylindrical Container Subjected to a Vertical Excitation

Singular perturbation theory of two-time scale expansions was developed both in inviscid and weak viscous fluids to investigate the motion of single surface standing wave in a liquid-filled circular cylindrical vessel, which is subject to a vertical periodical oscillation. Firstly, it is assumed that the fluid in the circular cylindrical vessel is inviscid, incompressible and the motion is irrotational, a nonlinear evolution equation of slowly varying complex amplitude, which incorporates cubic nonlinear term, external excitation and the influence of surface tension, was derived from solvability condition of high-order approximation. It shows that when forced frequency is low, the effect of surface tension on mode selection of surface wave is not important. However, when forced frequency is high, the influence of surface tension is significant, and can not be neglected. This proved that the surface tension has the function, which causes free surface returning to equilibrium location. Theoretical results much close to experimental results when the surface tension is considered. In fact, the damping will appear in actual physical system due to dissipation of viscosity of fluid. Based upon weakly viscous fluids assumption, the fluid field was divided into an outer potential flow region and an inner boundary layer region. A linear amplitude equation of slowly varying complex amplitude, which incorporates damping term and external excitation, was derived from linearized Navier-Stokes equation. The analytical expression of damping coefficient was determined and the relation between damping and other related parameters (such as viscosity, forced amplitude and depth of fluid) was presented. The nonlinear amplitude equation and a dispersion, which had been derived from the inviscid fluid approximation, were modified by adding linear damping. It was found that the modified results much reasonably close to experimental results. Moreover, the influence both of the surface tension and the weak viscosity on the mode formation was described by comparing theoretical and experimental results. The results show that when the forcing frequency is low, the viscosity of the fluid is prominent for the mode selection. However, when the forcing frequency is high, the surface tension of the fluid is prominent. Finally, instability of the surface wave is analyzed and properties of the solutions of the modified amplitude equation are determined together with phase-plane trajectories. A necessary condition of forming stable surface wave is obtained and unstable regions are illustrated. (c) 2005 Elsevier SAS. All rights reserved.

Relating thermodynamics to information theory : the equality of free energy and mutual information

In this thesis we uncover a new relation which links thermodynamics and information theory. We consider time as a channel and the detailed state of a physical system as a message. As the system evolves with time, ever present noise insures that the "message" is corrupted. Thermodynamic free energy measures the approach of the system toward equilibrium. Information theoretical mutual information measures the loss of memory of initial state. We regard the free energy and the mutual information as operators which map probability distributions over state space to real numbers. In the limit of long times, we show how the free energy operator and the mutual information operator asymptotically attain a very simple relationship to one another. This relationship is founded on the common appearance of entropy in the two operators and on an identity between internal energy and conditional entropy. The use of conditional entropy is what distinguishes our approach from previous efforts to relate thermodynamics and information theory.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Nonlinear dynamic transfer functions for certain retinal neuronal systems

The applicability of the white-noise method to the identification of a nonlinear system is investigated. Subsequently, the method is applied to certain vertebrate retinal neuronal systems and nonlinear, dynamic transfer functions are derived which describe quantitatively the information transformations starting with the light-pattern stimulus and culminating in the ganglion response which constitutes the visually-derived input to the brain. The retina of the catfish, Ictalurus punctatus, is used for the experiments.

The Wiener formulation of the white-noise theory is shown to be impractical and difficult to apply to a physical system. A different formulation based on crosscorrelation techniques is shown to be applicable to a wide range of physical systems provided certain considerations are taken into account. These considerations include the time-invariancy of the system, an optimum choice of the white-noise input bandwidth, nonlinearities that allow a representation in terms of a small number of characterizing kernels, the memory of the system and the temporal length of the characterizing experiment. Error analysis of the kernel estimates is made taking into account various sources of error such as noise at the input and output, bandwidth of white-noise input and the truncation of the gaussian by the apparatus.

Nonlinear transfer functions are obtained, as sets of kernels, for several neuronal systems: Light → Receptors, Light → Horizontal, Horizontal → Ganglion, Light → Ganglion and Light → ERG. The derived models can predict, with reasonable accuracy, the system response to any input. Comparison of model and physical system performance showed close agreement for a great number of tests, the most stringent of which is comparison of their responses to a white-noise input. Other tests include step and sine responses and power spectra.

Many functional traits are revealed by these models. Some are: (a) the receptor and horizontal cell systems are nearly linear (small signal) with certain "small" nonlinearities, and become faster (latency-wise and frequency-response-wise) at higher intensity levels, (b) all ganglion systems are nonlinear (half-wave rectification), (c) the receptive field center to ganglion system is slower (latency-wise and frequency-response-wise) than the periphery to ganglion system, (d) the lateral (eccentric) ganglion systems are just as fast (latency and frequency response) as the concentric ones, (e) (bipolar response) = (input from receptors) - (input from horizontal cell), (f) receptive field center and periphery exert an antagonistic influence on the ganglion response, (g) implications about the origin of ERG, and many others.

An analytical solution is obtained for the spatial distribution of potential in the S-space, which fits very well experimental data. Different synaptic mechanisms of excitation for the external and internal horizontal cells are implied.

Methods for melting temperature calculation

Melting temperature calculation has important applications in the theoretical study of phase diagrams and computational materials screenings. In this thesis, we present two new methods, i.e., the improved Widom's particle insertion method and the small-cell coexistence method, which we developed in order to capture melting temperatures both accurately and quickly.

We propose a scheme that drastically improves the efficiency of Widom's particle insertion method by efficiently sampling cavities while calculating the integrals providing the chemical potentials of a physical system. This idea enables us to calculate chemical potentials of liquids directly from first-principles without the help of any reference system, which is necessary in the commonly used thermodynamic integration method. As an example, we apply our scheme, combined with the density functional formalism, to the calculation of the chemical potential of liquid copper. The calculated chemical potential is further used to locate the melting temperature. The calculated results closely agree with experiments.

We propose the small-cell coexistence method based on the statistical analysis of small-size coexistence MD simulations. It eliminates the risk of a metastable superheated solid in the fast-heating method, while also significantly reducing the computer cost relative to the traditional large-scale coexistence method. Using empirical potentials, we validate the method and systematically study the finite-size effect on the calculated melting points. The method converges to the exact result in the limit of a large system size. An accuracy within 100 K in melting temperature is usually achieved when the simulation contains more than 100 atoms. DFT examples of Tantalum, high-pressure Sodium, and ionic material NaCl are shown to demonstrate the accuracy and flexibility of the method in its practical applications. The method serves as a promising approach for large-scale automated material screening in which the melting temperature is a design criterion.

We present in detail two examples of refractory materials. First, we demonstrate how key material properties that provide guidance in the design of refractory materials can be accurately determined via ab initio thermodynamic calculations in conjunction with experimental techniques based on synchrotron X-ray diffraction and thermal analysis under laser-heated aerodynamic levitation. The properties considered include melting point, heat of fusion, heat capacity, thermal expansion coefficients, thermal stability, and sublattice disordering, as illustrated in a motivating example of lanthanum zirconate (La₂Zr₂O₇). The close agreement with experiment in the known but structurally complex compound La₂Zr₂O₇ provides good indication that the computation methods described can be used within a computational screening framework to identify novel refractory materials. Second, we report an extensive investigation into the melting temperatures of the Hf-C and Hf-Ta-C systems using ab initio calculations. With melting points above 4000 K, hafnium carbide (HfC) and tantalum carbide (TaC) are among the most refractory binary compounds known to date. Their mixture, with a general formula Ta_xHf_1-xC_y, is known to have a melting point of 4215 K at the composition Ta₄HfC₅, which has long been considered as the highest melting temperature for any solid. Very few measurements of melting point in tantalum and hafnium carbides have been documented, because of the obvious experimental difficulties at extreme temperatures. The investigation lets us identify three major chemical factors that contribute to the high melting temperatures. Based on these three factors, we propose and explore a new class of materials, which, according to our ab initio calculations, may possess even higher melting temperatures than Ta-Hf-C. This example also demonstrates the feasibility of materials screening and discovery via ab initio calculations for the optimization of "higher-level" properties whose determination requires extensive sampling of atomic configuration space.

Phase transitions from the solid state of monatomic elements

The principle aims of this thesis include the development of models of sublimation and melting from first principles and the application of these models to the rare gases.

A simple physical model is constructed to represent the sublimation of monatomic elements. According to this model, the solid and gas phases are two states of a single physical system. The nature of the phase transition is clearly revealed, and the relations between the vapor pressure, the latent heat, and the transition temperature are derived. The resulting theory is applied to argon, krypton, and xenon, and good agreement with experiment is found.

For the melting transition, the solid is represented by an anharmonic model and the liquid is described by the Percus-Yevick approximation. The behavior of the liquid at high densities is studied on the isotherms kT/∈ = 1.3, 1.8, and 2.0, where k is Boltzmann's constant, T is the temperature, and e is the well depth of the Lennard-Jones 12-6 pair potential. No solutions of the PercusYevick equation were found for ρσ³ above 1.3, where ρ is the particle density and σ is the radial parameter of the Lennard-Jones potential. The liquid structure is found to be very different from the solid structure near the melting line. The liquid pressures are about 50 percent low for experimental melting densities of argon. This discrepancy gives rise to melting pressures up to twice the experimental values.

Response of linear, viscous damped systems to excitations having time-varying frequency

The response of linear, viscous damped systems to excitations having time-varying frequency is the subject of exact and approximate analyses, which are supplemented by an analog computer study of single degree of freedom system response to excitations having frequencies depending linearly and exponentially on time.

The technique of small perturbations and the methods of stationary phase and saddle-point integration, as well as a novel bounding procedure, are utilized to derive approximate expressions characterizing the system response envelope—particularly near resonances—for the general time-varying excitation frequency.

Descriptive measurements of system resonant behavior recorded during the course of the analog study—maximum response, excitation frequency at which maximum response occurs, and the width of the response peak at the half-power level—are investigated to determine dependence upon natural frequency, damping, and the functional form of the excitation frequency.

The laboratory problem of determining the properties of a physical system from records of its response to excitations of this class is considered, and the transient phenomenon known as “ringing” is treated briefly.

It is shown that system resonant behavior, as portrayed by the above measurements and expressions, is relatively insensitive to the specifics of the excitation frequency-time relation and may be described to good order in terms of parameters combining system properties with the time derivative of excitation frequency evaluated at resonance.

One of these parameters is shown useful for predicting whether or not a given excitation having a time-varying frequency will produce strong or subtle changes in the response envelope of a given system relative to the steady-state response envelope. The parameter is shown, additionally, to be useful for predicting whether or not a particular response record will exhibit the “ringing” phenomenon.

Cryogenic Silicon Optical Reference Cavities

Thermodynamical fluctuations in temperature and position exist in every physical system, and show up as a fundamental noise limit whenever we choose to measure some quantity in a laboratory environment. Thermodynamical fluctuations in the position of the atoms in the dielectric coatings on the mirrors for optical cavities at the forefront of precision metrology (e.g., LIGO, the cavities which probe atomic transitions to define the second) are a current limiting noise source for these experiments, and anything which involves locking a laser to an optical cavity. These thermodynamic noise sources scale physical geometry of experiment, material properties (such as mechanical loss in our dielectric coatings), and temperature. The temperature scaling provides a natural motivation to move to lower temperatures, with a potential huge benefit for redesigning a room temperature experiment which is limited by thermal noise for cryogenic operation.

We design, build, and characterize a pair of linear Fabry-Perot cavities to explore limitations to ultra low noise laser stabilization experiments at cryogenic temperatures. We use silicon as the primary material for the cavity and mirrors, due to a zero crossing in its linear coefficient of thermal expansion (CTE) at 123 K, and other desirable material properties. We use silica tantala coatings, which are currently the best for making high finesse low noise cavities at room temperature. The material properties of these coating materials (which set the thermal noise levels) are relatively unknown at cryogenic temperatures, which motivates us to study them at these temperatures. We were not able to measure any thermal noise source with our experiment due to excess noise. In this work we analyze the design and performance of the cavities, and recommend a design shift from mid length cavities to short cavities in order to facilitate a direct measurement of cryogenic coating noise.

In addition, we measure the cavities (frequency dependent) photo-thermal response. This can help characterize thermooptic noise in the coatings, which is poorly understood at cryogenic temperatures. We also explore the feasibility of using the cavity to do macroscopic quantum optomechanics such as ground state cooling.

Ocupação dos solos em terrenos marginais às lagoas costeiras: mudanças e perspectivas ambientais frente à expansão urbana - o caso da lagoa de Jacarepaguá (Rio de Janeiro)

O objetivo do trabalho é analisar a lagoa de Jacarepaguá e a ocupação no seu entorno de forma multitemporal, contribuindo para o melhor entendimento das atuais condições ambientais da Baixada de Jacarepaguá. A metodologia adotada buscou identificar mudanças físicas do meio a partir 1980 através da elaboração, comparação e análise de mapas de ocupação e uso dos solos relativos aos anos de 1984, 1992, 2001 e 2010, e da identificação da qualidade da água da lagoa de Jacarepaguá, das suas condições de profundidade, tamanho do espelho dágua e de sua relação com a população local. Com isso foi possível retratar formas de integração entre os processos naturais e sociais em um dado espaço-tempo assim como estabelecer tendências futuras desse ambiente. Os resultados mostram que de tempos em tempos há uma refuncionalização do espaço, que se reflete não só na conformação dos terrenos marginais alagadiços mas também nas condições físicas da própria lagoa de Jacarepaguá. Seu espelho dágua vem sendo confinado pelas formas de ocupação nas áreas das bacias fluviais e nos seus terrenos marginais (impermeabilização, aterros e obras de drenagem) fazendo com que haja uma estabilidade relativa na sua dimensão areal e também no volume de suas águas. A lagoa apresenta dados históricos de poluição por esgoto doméstico que têm acelerado suas condições naturais de assoreamento e comprometido à qualidade de suas águas. E mesmo havendo projetos e obras de saneamento para o local, verifica-se que tem havido um aumento da poluição da lagoa principalmente na sua porção oeste, conforme o resultado das análises realizadas com os dados temporais disponíveis de DBO, fósforo, Nitrogênio Kj, OD e salinidade. Isto pode ser explicado pela tendência atual da expansão urbana rumo a essa direção. Constatou-se que apesar de, por algum tempo, os tipos de terreno terem condicionado as formas de ocupação, atualmente o processo se inverteu, sendo a ocupação indutora e recondicionante da estruturação do meio. São apresentadas e caracterizadas diversas formas e respectivos tipos de usos do solo na área. Conclui-se que as condições ambientais da lagoa de Jacarepaguá e suas perspectivas futuras dependem atualmente mais da forma com que a sociedade quer e pretende incorpora-la ao seu ambiente do que da dinâmica natural do sistema físico do qual faz parte.

Improving discharge characteristics of indirect integral collector storage systems with multi-element storage

Desired performance of unpressurized integral collector storage systems hinges on the appropriate selection of storage volume and the immersed heat exchanger. This paper presents analytical results expressing the relation between storage volume, number of heat exchanger transfer units and temperature limited performance. For a system composed of a single storage element, the limiting behavior of a perfectly stratified storage element is shown to be superior to a fully-mixed storage element, consistent with more general analysis of thermal storage. Since, however, only the fully-mixed limit is readily obtainable in a physical system, the present paper also examines a division of the storage volume into separate compartments. This multi-element storage system shows significantly improved discharge characteristics as a result of improved elemental area utilization and temperature variation between elements, comparable in many cases to a single perfectly-stratified storage element. In addition, the multi-element system shows increased robustness with respect to variations in heat exchanger effectiveness and initial storage temperature.

Sparse recovery of complex phase-encoded velocity images using iterative thresholding

In this paper we propose a new algorithm for reconstructing phase-encoded velocity images of catalytic reactors from undersampled NMR acquisitions. Previous work on this application has employed total variation and nonlinear conjugate gradients which, although promising, yields unsatisfactory, unphysical visual results. Our approach leverages prior knowledge about the piecewise-smoothness of the phase map and physical constraints imposed by the system under study. We show how iteratively regularizing the real and imaginary parts of the acquired complex image separately in a shift-invariant wavelet domain works to produce a piecewise-smooth velocity map, in general. Using appropriately defined metrics we demonstrate higher fidelity to the ground truth and physical system constraints than previous methods for this specific application. © 2013 IEEE.

Cognition from the bottom up: on biological inspiration, body morphology, and soft materials.

Traditionally, in cognitive science the emphasis is on studying cognition from a computational point of view. Studies in biologically inspired robotics and embodied intelligence, however, provide strong evidence that cognition cannot be analyzed and understood by looking at computational processes alone, but that physical system-environment interaction needs to be taken into account. In this opinion article, we review recent progress in cognitive developmental science and robotics, and expand the notion of embodiment to include soft materials and body morphology in the big picture. We argue that we need to build our understanding of cognition from the bottom up; that is, all the way from how our body is physically constructed.