Damage detection in civil structures using high-frequency seismograms

The dynamic properties of a structure are a function of its physical properties, and changes in the physical properties of the structure, including the introduction of structural damage, can cause changes in its dynamic behavior. Structural health monitoring (SHM) and damage detection methods provide a means to assess the structural integrity and safety of a civil structure using measurements of its dynamic properties. In particular, these techniques enable a quick damage assessment following a seismic event. In this thesis, the application of high-frequency seismograms to damage detection in civil structures is investigated.

Two novel methods for SHM are developed and validated using small-scale experimental testing, existing structures in situ, and numerical testing. The first method is developed for pre-Northridge steel-moment-resisting frame buildings that are susceptible to weld fracture at beam-column connections. The method is based on using the response of a structure to a nondestructive force (i.e., a hammer blow) to approximate the response of the structure to a damage event (i.e., weld fracture). The method is applied to a small-scale experimental frame, where the impulse response functions of the frame are generated during an impact hammer test. The method is also applied to a numerical model of a steel frame, in which weld fracture is modeled as the tensile opening of a Mode I crack. Impulse response functions are experimentally obtained for a steel moment-resisting frame building in situ. Results indicate that while acceleration and velocity records generated by a damage event are best approximated by the acceleration and velocity records generated by a colocated hammer blow, the method may not be robust to noise. The method seems to be better suited for damage localization, where information such as arrival times and peak accelerations can also provide indication of the damage location. This is of significance for sparsely-instrumented civil structures.

The second SHM method is designed to extract features from high-frequency acceleration records that may indicate the presence of damage. As short-duration high-frequency signals (i.e., pulses) can be indicative of damage, this method relies on the identification and classification of pulses in the acceleration records. It is recommended that, in practice, the method be combined with a vibration-based method that can be used to estimate the loss of stiffness. Briefly, pulses observed in the acceleration time series when the structure is known to be in an undamaged state are compared with pulses observed when the structure is in a potentially damaged state. By comparing the pulse signatures from these two situations, changes in the high-frequency dynamic behavior of the structure can be identified, and damage signals can be extracted and subjected to further analysis. The method is successfully applied to a small-scale experimental shear beam that is dynamically excited at its base using a shake table and damaged by loosening a screw to create a moving part. Although the damage is aperiodic and nonlinear in nature, the damage signals are accurately identified, and the location of damage is determined using the amplitudes and arrival times of the damage signal. The method is also successfully applied to detect the occurrence of damage in a test bed data set provided by the Los Alamos National Laboratory, in which nonlinear damage is introduced into a small-scale steel frame by installing a bumper mechanism that inhibits the amount of motion between two floors. The method is successfully applied and is robust despite a low sampling rate, though false negatives (undetected damage signals) begin to occur at high levels of damage when the frequency of damage events increases. The method is also applied to acceleration data recorded on a damaged cable-stayed bridge in China, provided by the Center of Structural Monitoring and Control at the Harbin Institute of Technology. Acceleration records recorded after the date of damage show a clear increase in high-frequency short-duration pulses compared to those previously recorded. One undamage pulse and two damage pulses are identified from the data. The occurrence of the detected damage pulses is consistent with a progression of damage and matches the known chronology of damage.

Towards conditional RNAi : shape and sequence transduction with small conditional RNAs

RNA interference (RNAi) is a powerful biological pathway allowing for sequence-specific knockdown of any gene of interest. While RNAi is a proven tool for probing gene function in biological circuits, it is limited by being constitutively ON and executes the logical operation: silence gene Y. To provide greater control over post-transcriptional gene silencing, we propose engineering a biological logic gate to implement “conditional RNAi.” Such a logic gate would silence gene Y only upon the expression of gene X, a completely unrelated gene, executing the logic: if gene X is transcribed, silence independent gene Y. Silencing of gene Y could be confined to a specific time and/or tissue by appropriately selecting gene X.

To implement the logic of conditional RNAi, we present the design and experimental validation of three nucleic acid self-assembly mechanisms which detect a sub-sequence of mRNA X and produce a Dicer substrate specific to gene Y. We introduce small conditional RNAs (scRNAs) to execute the signal transduction under isothermal conditions. scRNAs are small RNAs which change conformation, leading to both shape and sequence signal transduction, in response to hybridization to an input nucleic acid target. While all three conditional RNAi mechanisms execute the same logical operation, they explore various design alternatives for nucleic acid self-assembly pathways, including the use of duplex and monomer scRNAs, stable versus metastable reactants, multiple methods of nucleation, and 3-way and 4-way branch migration.

We demonstrate the isothermal execution of the conditional RNAi mechanisms in a test tube with recombinant Dicer. These mechanisms execute the logic: if mRNA X is detected, produce a Dicer substrate targeting independent mRNA Y. Only the final Dicer substrate, not the scRNA reactants or intermediates, is efficiently processed by Dicer. Additional work in human whole-cell extracts and a model tissue-culture system delves into both the promise and challenge of implementing conditional RNAi in vivo.

An investigation of detached shock waves

This investigation demonstrates an application of a flexible wall nozzle for testing in a supersonic wind tunnel. It is conservative to say that the versatility of this nozzle is such that it warrants the expenditure of time to carefully engineer a nozzle and incorporate it in the wind tunnel as a permanent part of the system. The gradients in the test section were kept within one percent of the calibrated Mach number, however, the gradients occurring over the bodies tested were only ± 0.2 percent in Mach number.

The conditions existing on a finite cone with a vertex angle of 75° were investigated by considering the pressure distribution on the cone and the shape of the shock wave. The pressure distribution on the surface of the 75° cone when based on upstream conditions does not show any discontinuities at the theoretical attachment Mach number.

Both the angle of the shock wave and the pressure distribution of the 75° cone are in very close agreement with the theoretical values given in the Kopal report, (Ref. 3).

The location of the intersection of the sonic line with the surface of the cone and with the shock wave are given for the cone. The blocking characteristics of the GALCIT supersonic wind tunnel were investigated with a series of 60° cones.

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.