Collective behavior of asperities as a model for friction and adhesion

Understanding friction and adhesion in static and sliding contact of surfaces is important in numerous physical phenomena and technological applications. Most surfaces are rough at the microscale, and thus the real area of contact is only a fraction of the nominal area. The macroscopic frictional and adhesive response is determined by the collective behavior of the population of evolving and interacting microscopic contacts. This collective behavior can be very different from the behavior of individual contacts. It is thus important to understand how the macroscopic response emerges from the microscopic one. In this thesis, we develop a theoretical and computational framework to study the collective behavior. Our philosophy is to assume a simple behavior of a single asperity and study the collective response of an ensemble. Our work bridges the existing well-developed studies of single asperities with phenomenological laws that describe macroscopic rate-and-state behavior of frictional interfaces. We find that many aspects of the macroscopic behavior are robust with respect to the microscopic response. This explains why qualitatively similar frictional features are seen for a diverse range of materials. We first show that the collective response of an ensemble of one-dimensional independent viscoelastic elements interacting through a mean field reproduces many qualitative features of static and sliding friction evolution. The resulting macroscopic behavior is different from the microscopic one: for example, even if each contact is velocity-strengthening, the macroscopic behavior can be velocity-weakening. The framework is then extended to incorporate three-dimensional rough surfaces, long- range elastic interactions between contacts, and time-dependent material behaviors such as viscoelasticity and viscoplasticity. Interestingly, the mean field behavior dominates and the elastic interactions, though important from a quantitative perspective, do not change the qualitative macroscopic response. Finally, we examine the effect of adhesion on the frictional response as well as develop a force threshold model for adhesion and mode I interfacial cracks.

Establishing the C. elegans uterine seam cell (utse) as a novel model for studying cell behavior

The molecular inputs necessary for cell behavior are vital to our understanding of development and disease. Proper cell behavior is necessary for processes ranging from creating one’s face (neural crest migration) to spreading cancer from one tissue to another (invasive metastatic cancers). Identifying the genes and tissues involved in cell behavior not only increases our understanding of biology but also has the potential to create targeted therapies in diseases hallmarked by aberrant cell behavior.

A well-characterized model system is key to determining the molecular and spatial inputs necessary for cell behavior. In this work I present the C. elegans uterine seam cell (utse) as an ideal model for studying cell outgrowth and shape change. The utse is an H-shaped cell within the hermaphrodite uterus that functions in attaching the uterus to the body wall. Over L4 larval stage, the utse grows bidirectionally along the anterior-posterior axis, changing from an ellipsoidal shape to an elongated H-shape. Spatially, the utse requires the presence of the uterine toroid cells, sex muscles, and the anchor cell nucleus in order to properly grow outward. Several gene families are involved in utse development, including Trio, Nav, Rab GTPases, Arp2/3, as well as 54 other genes found from a candidate RNAi screen. The utse can be used as a model system for studying metastatic cancer. Meprin proteases are involved in promoting invasiveness of metastatic cancers and the meprin-likw genes nas-21, nas-22, and toh-1 act similarly within the utse. Studying nas-21 activity has also led to the discovery of novel upstream inhibitors and activators as well as targets of nas-21, some of which have been characterized to affect meprin activity. This illustrates that the utse can be used as an in vivo model for learning more about meprins, as well as various other proteins involved in metastasis.

The biological sense of smell: olfactory search behavior and a metabolic view for olfactory perception

Part I of the thesis describes the olfactory searching and scanning behaviors of rats in a wind tunnel, and a detailed movement analysis of terrestrial arthropod olfactory scanning behavior. Olfactory scanning behaviors in rats may be a behavioral correlate to hippocampal place cell activity.

Part II focuses on the organization of olfactory perception, what it suggests about a natural order for chemicals in the environment, and what this in tum suggests about the organization of the olfactory system. A model of odor quality space (analogous to the "color wheel") is presented. This model defines relationships between odor qualities perceived by human subjects based on a quantitative similarity measure. Compounds containing Carbon, Nitrogen, or Sulfur elicit odors that are contiguous in this odor representation, which thus allows one to predict the broad class of odor qualities a compound is likely to elicit. Based on these findings, a natural organization for olfactory stimuli is hypothesized: the order provided by the metabolic process. This hypothesis is tested by comparing compounds that are structurally similar, perceptually similar, and metabolically similar in a psychophysical cross-adaptation paradigm. Metabolically similar compounds consistently evoked shifts in odor quality and intensity under cross-adaptation, while compounds that were structurally similar or perceptually similar did not. This suggests that the olfactory system may process metabolically similar compounds using the same neural pathways, and that metabolic similarity may be the fundamental metric about which olfactory processing is organized. In other words, the olfactory system may be organized around a biological basis.

The idea of a biological basis for olfactory perception represents a shift in how olfaction is understood. The biological view has predictive power while the current chemical view does not, and the biological view provides explanations for some of the most basic questions in olfaction, that are unanswered in the chemical view. Existing data do not disprove a biological view, and are consistent with basic hypotheses that arise from this viewpoint.

The strategic behavior of rational novices

There is a growing amount of experimental evidence that suggests people often deviate from the predictions of game theory. Some scholars attempt to explain the observations by introducing errors into behavioral models. However, most of these modifications are situation dependent and do not generalize. A new theory, called the rational novice model, is introduced as an attempt to provide a general theory that takes account of erroneous behavior. The rational novice model is based on two central principals. The first is that people systematically make inaccurate guesses when they are evaluating their options in a game-like situation. The second is that people treat their decisions similar to a portfolio problem. As a result, non optimal actions in a game theoretic sense may be included in the rational novice strategy profile with positive weights.

The rational novice model can be divided into two parts: the behavioral model and the equilibrium concept. In a theoretical chapter, the mathematics of the behavioral model and the equilibrium concept are introduced. The existence of the equilibrium is established. In addition, the Nash equilibrium is shown to be a special case of the rational novice equilibrium. In another chapter, the rational novice model is applied to a voluntary contribution game. Numerical methods were used to obtain the solution. The model is estimated with data obtained from the Palfrey and Prisbrey experimental study of the voluntary contribution game. It is found that the rational novice model explains the data better than the Nash model. Although a formal statistical test was not used, pseudo R^2 analysis indicates that the rational novice model is better than a Probit model similar to the one used in the Palfrey and Prisbrey study.

The rational novice model is also applied to a first price sealed bid auction. Again, computing techniques were used to obtain a numerical solution. The data obtained from the Chen and Plott study were used to estimate the model. The rational novice model outperforms the CRRAM, the primary Nash model studied in the Chen and Plott study. However, the rational novice model is not the best amongst all models. A sophisticated rule-of-thumb, called the SOPAM, offers the best explanation of the data.

Earthquakes of the Nepal Himalaya : towards a physical model of the seismic cycle

Home to hundreds of millions of souls and land of excessiveness, the Himalaya is also the locus of a unique seismicity whose scope and peculiarities still remain to this day somewhat mysterious. Having claimed the lives of kings, or turned ancient timeworn cities into heaps of rubbles and ruins, earthquakes eerily inhabit Nepalese folk tales with the fatalistic message that nothing lasts forever. From a scientific point of view as much as from a human perspective, solving the mysteries of Himalayan seismicity thus represents a challenge of prime importance. Documenting geodetic strain across the Nepal Himalaya with various GPS and leveling data, we show that unlike other subduction zones that exhibit a heterogeneous and patchy coupling pattern along strike, the last hundred kilometers of the Main Himalayan Thrust fault, or MHT, appear to be uniformly locked, devoid of any of the “creeping barriers” that traditionally ward off the propagation of large events. The approximately 20 mm/yr of reckoned convergence across the Himalaya matching previously established estimates of the secular deformation at the front of the arc, the slip accumulated at depth has to somehow elastically propagate all the way to the surface at some point. And yet, neither large events from the past nor currently recorded microseismicity nearly compensate for the massive moment deficit that quietly builds up under the giant mountains. Along with this large unbalanced moment deficit, the uncommonly homogeneous coupling pattern on the MHT raises the question of whether or not the locked portion of the MHT can rupture all at once in a giant earthquake. Univocally answering this question appears contingent on the still elusive estimate of the magnitude of the largest possible earthquake in the Himalaya, and requires tight constraints on local fault properties. What makes the Himalaya enigmatic also makes it the potential source of an incredible wealth of information, and we exploit some of the oddities of Himalayan seismicity in an effort to improve the understanding of earthquake physics and cipher out the properties of the MHT. Thanks to the Himalaya, the Indo-Gangetic plain is deluged each year under a tremendous amount of water during the annual summer monsoon that collects and bears down on the Indian plate enough to pull it away from the Eurasian plate slightly, temporarily relieving a small portion of the stress mounting on the MHT. As the rainwater evaporates in the dry winter season, the plate rebounds and tension is increased back on the fault. Interestingly, the mild waggle of stress induced by the monsoon rains is about the same size as that from solid-Earth tides which gently tug at the planets solid layers, but whereas changes in earthquake frequency correspond with the annually occurring monsoon, there is no such correlation with Earth tides, which oscillate back-and-forth twice a day. We therefore investigate the general response of the creeping and seismogenic parts of MHT to periodic stresses in order to link these observations to physical parameters. First, the response of the creeping part of the MHT is analyzed with a simple spring-and-slider system bearing rate-strengthening rheology, and we show that at the transition with the locked zone, where the friction becomes near velocity neutral, the response of the slip rate may be amplified at some periods, which values are analytically related to the physical parameters of the problem. Such predictions therefore hold the potential of constraining fault properties on the MHT, but still await observational counterparts to be applied, as nothing indicates that the variations of seismicity rate on the locked part of the MHT are the direct expressions of variations of the slip rate on its creeping part, and no variations of the slip rate have been singled out from the GPS measurements to this day. When shifting to the locked seismogenic part of the MHT, spring-and-slider models with rate-weakening rheology are insufficient to explain the contrasted responses of the seismicity to the periodic loads that tides and monsoon both place on the MHT. Instead, we resort to numerical simulations using the Boundary Integral CYCLes of Earthquakes algorithm and examine the response of a 2D finite fault embedded with a rate-weakening patch to harmonic stress perturbations of various periods. We show that such simulations are able to reproduce results consistent with a gradual amplification of sensitivity as the perturbing period get larger, up to a critical period corresponding to the characteristic time of evolution of the seismicity in response to a step-like perturbation of stress. This increase of sensitivity was not reproduced by simple 1D-spring-slider systems, probably because of the complexity of the nucleation process, reproduced only by 2D-fault models. When the nucleation zone is close to its critical unstable size, its growth becomes highly sensitive to any external perturbations and the timings of produced events may therefore find themselves highly affected. A fully analytical framework has yet to be developed and further work is needed to fully describe the behavior of the fault in terms of physical parameters, which will likely provide the keys to deduce constitutive properties of the MHT from seismological observations.

The short-timescale behavior of glacial ice

Glaciers are often assumed to deform only at slow (i.e., glacial) rates. However, with the advent of high rate geodetic observations of ice motion, many of the intricacies of glacial deformation on hourly and daily timescales have been observed and quantified. This thesis explores two such short timescale processes: the tidal perturbation of ice stream motion and the catastrophic drainage of supraglacial meltwater lakes. Our investigation into the transmission length-scale of a tidal load represents the first study to explore the daily tidal influence on ice stream motion using three-dimensional models. Our results demonstrate both that the implicit assumptions made in the standard two-dimensional flow-line models are inherently incorrect for many ice streams, and that the anomalously large spatial extent of the tidal influence seen on the motion of some glaciers cannot be explained, as previously thought, through the elastic or viscoelastic transmission of tidal loads through the bulk of the ice stream. We then discuss how the phase delay between a tidal forcing and the ice stream’s displacement response can be used to constrain in situ viscoelastic properties of glacial ice. Lastly, for the problem of supraglacial lake drainage, we present a methodology for implementing linear viscoelasticity into an existing model for lake drainage. Our work finds that viscoelasticity is a second-order effect when trying to model the deformation of ice in response to a meltwater lake draining to a glacier’s bed. The research in this thesis demonstrates that the first-order understanding of the short-timescale behavior of naturally occurring ice is incomplete, and works towards improving our fundamental understanding of ice behavior over the range of hours to days.

Coupled effects of mechanics, geometry, and chemistry on bio-membrane behavior

Lipid bilayer membranes are models for cell membranes--the structure that helps regulate cell function. Cell membranes are heterogeneous, and the coupling between composition and shape gives rise to complex behaviors that are important to regulation. This thesis seeks to systematically build and analyze complete models to understand the behavior of multi-component membranes.

We propose a model and use it to derive the equilibrium and stability conditions for a general class of closed multi-component biological membranes. Our analysis shows that the critical modes of these membranes have high frequencies, unlike single-component vesicles, and their stability depends on system size, unlike in systems undergoing spinodal decomposition in flat space. An important implication is that small perturbations may nucleate localized but very large deformations. We compare these results with experimental observations.

We also study open membranes to gain insight into long tubular membranes that arise for example in nerve cells. We derive a complete system of equations for open membranes by using the principle of virtual work. Our linear stability analysis predicts that the tubular membranes tend to have coiling shapes if the tension is small, cylindrical shapes if the tension is moderate, and beading shapes if the tension is large. This is consistent with experimental observations reported in the literature in nerve fibers. Further, we provide numerical solutions to the fully nonlinear equilibrium equations in some problems, and show that the observed mode shapes are consistent with those suggested by linear stability. Our work also proves that beadings of nerve fibers can appear purely as a mechanical response of the membrane.

Catalytic conversion of nitrogen to ammonia by an iron model complex

Threefold symmetric Fe phosphine complexes have been used to model the structural and functional aspects of biological N₂ fixation by nitrogenases. Low-valent bridging Fe-S-Fe complexes in the formal oxidation states Fe(II)Fe(II), Fe(II)/Fe(I), and Fe(I)/Fe(I) have been synthesized which display rich spectroscopic and magnetic behavior. A series of cationic tris-phosphine borane (TPB) ligated Fe complexes have been synthesized and been shown to bind a variety of nitrogenous ligands including N₂H₄, NH₃, and NH₂-. These complexes are all high spin S = 3/2 and display EPR and magnetic characteristics typical of this spin state. Furthermore, a sequential protonation and reduction sequence of a terminal amide results in loss of NH₃ and uptake of N₂. These stoichiometric transformations represent the final steps in potential N₂ fixation schemes.

Treatment of an anionic FeN₂ complex with excess acid also results in the formation of some NH₃, suggesting the possibility of a catalytic cycle for the conversion of N₂ to NH₃ mediated by Fe. Indeed, use of excess acid and reductant results in the formation of seven equivalents of NH₃ per Fe center, demonstrating Fe mediated catalytic N₂ fixation with acids and protons for the first time. Numerous control experiments indicate that this catalysis is likely being mediated by a molecular species.

A number of other phosphine ligated Fe complexes have also been tested for catalysis and suggest that a hemi-labile Fe-B interaction may be critical for catalysis. Additionally, various conditions for the catalysis have been investigated. These studies further support the assignment of a molecular species and delineate some of the conditions required for catalysis.

Finally, combined spectroscopic studies have been performed on a putative intermediate for catalysis. These studies converge on an assignment of this new species as a hydrazido(2-) complex. Such species have been known on group 6 metals for some time, but this represents the first characterization of this ligand on Fe. Further spectroscopic studies suggest that this species is present in catalytic mixtures, which suggests that the first steps of a distal mechanism for N₂ fixation are feasible in this system.

A model of the olfactory bulb and beyond

The olfactory bulb of mammals aids in the discrimination of odors. A mathematical model based on the bulbar anatomy and electrophysiology is described. Simulations of the highly non-linear model produce a 35-60 Hz modulated activity, which is coherent across the bulb. The decision states (for the odor information) in this system can be thought of as stable cycles, rather than as point stable states typical of simpler neuro-computing models. Analysis shows that a group of coupled non-linear oscillators are responsible for the oscillatory activities. The output oscillation pattern of the bulb is determined by the odor input. The model provides a framework in which to understand the transformation between odor input and bulbar output to the olfactory cortex. This model can also be extended to other brain areas such as the hippocampus, thalamus, and neocortex, which show oscillatory neural activities. There is significant correspondence between the model behavior and observed electrophysiology.

It has also been suggested that the olfactory bulb, the first processing center after the sensory cells in the olfactory pathway, plays a role in olfactory adaptation, odor sensitivity enhancement by motivation, and other olfactory psychophysical phenomena. The input from the higher olfactory centers to the inhibitory cells in the bulb are shown to be able to modulate the response, and thus the sensitivity, of the bulb to odor input. It follows that the bulb can decrease its sensitivity to a pre-existing and detected odor (adaptation) while remaining sensitive to new odors, or can increase its sensitivity to discover interesting new odors. Other olfactory psychophysical phenomena such as cross-adaptation are also discussed.

Modeling and analysis of hysteretic structural behavior

For damaging response, the force-displacement relationship of a structure is highly nonlinear and history-dependent. For satisfactory analysis of such behavior, it is important to be able to characterize and to model the phenomenon of hysteresis accurately. A number of models have been proposed for response studies of hysteretic structures, some of which are examined in detail in this thesis. There are two popular classes of models used in the analysis of curvilinear hysteretic systems. The first is of the distributed element or assemblage type, which models the physical behavior of the system by using well-known building blocks. The second class of models is of the differential equation type, which is based on the introduction of an extra variable to describe the history dependence of the system.

Owing to their mathematical simplicity, the latter models have been used extensively for various applications in structural dynamics, most notably in the estimation of the response statistics of hysteretic systems subjected to stochastic excitation. But the fundamental characteristics of these models are still not clearly understood. A response analysis of systems using both the Distributed Element model and the differential equation model when subjected to a variety of quasi-static and dynamic loading conditions leads to the following conclusion: Caution must be exercised when employing the models belonging to the second class in structural response studies as they can produce misleading results.

The Massing's hypothesis, originally proposed for steady-state loading, can be extended to general transient loading as well, leading to considerable simplification in the analysis of the Distributed Element models. A simple, nonparametric identification technique is also outlined, by means of which an optimal model representation involving one additional state variable is determined for hysteretic systems.

Effect of pressure on mechanical behavior of filled elastomers

The Young's modulus, stress-strain curves, and failure properties of glass bead-filled EPDM vulcanizates were studied under superposed hydrostatic pressure. The glass bead-filled EPDM was employed as a representation of composite systems, and the hydrostatic pressure controls the filler-elastomer separation under deformation. This separation shows up as a volume change of the system, and its infuence is reflected in the mechanical behavior as a reinforcing effect of variable degree.

The strain energy stored in the composite system in simple tension was calculated by introducing a model which is described as a cylindrical block of elastomer with two half spheres of filler on each end with their centers on the axis of the cylinder. In the derivation of the strain energy, assumptions were made to obtain the strain distribution in the model, and strain energy-strain relation for the elastomer was also assumed. The derivation was carried out for the case of no filler-elastomer separation and was modified to include the case of filler-elastomer separation.

The resulting strain energy, as a function of stretch ratio and volume of the system, was used to obtain stress-strain curves and volume change-strain curves of composite systems under superposed hydrostatic pressure.

Changes in the force and the lateral dimension of a ring specimen were measured as it was stretched axially under a superposed hydrostatic pressure in order to calculate the mechanical properties mentioned above. A tensile tester was used which is capable of sealing the whole system to carry out a measurement under pressure. A thickness measuring device, based on the Hall effect, was built for the measurement of changes in the lateral dimension of a specimen.

The theoretical and experimental results of Young's modulus and stress-strain curves were compared and showed fairly good agreement.

The failure data were discussed in terms of failure surfaces, and it was concluded that a failure surface of the glass-bead-filled EPDM consists of two cones.

High pressure states in condensed matter: I. High pressure behavior of the iron-sulphur system with applications to the earth's core. II. Empirical equation of state for organic compounds at high pressures

Part I:

The earth's core is generally accepted to be composed primarily of iron, with an admixture of other elements. Because the outer core is observed not to transmit shear waves at seismic frequencies, it is known to be liquid or primarily liquid. A new equation of state is presented for liquid iron, in the form of parameters for the 4th order Birch-Murnaghan and Mie-Grüneisen equations of state. The parameters were constrained by a set of values for numerous properties compiled from the literature. A detailed theoretical model is used to constrain the P-T behavior of the heat capacity, based on recent advances in the understanding of the interatomic potentials for transition metals. At the reference pressure of 10⁵ Pa and temperature of 1811 K (the normal melting point of Fe), the parameters are: ρ = 7037 kg/m³, K_S0 = 110 GPa, K_S' = 4.53, K_S" = -.0337 GPa-1, and γ = 2.8, with γ α ρ^-1.17. Comparison of the properties predicted by this model with the earth model PREM indicates that the outer core is 8 to 10 % less dense than pure liquid Fe at the same conditions. The inner core is also found to be 3 to 5% less dense than pure liquid Fe, supporting the idea of a partially molten inner core. The density deficit of the outer core implies that the elements dissolved in the liquid Fe are predominantly of lower atomic weight than Fe. Of the candidate light elements favored by researchers, only sulfur readily dissolves into Fe at low pressure, which means that this element was almost certainly concentrated in the core at early times. New melting data are presented for FeS and FeS₂ which indicate that the FeS₂ is the S-hearing liquidus solid phase at inner core pressures. Consideration of the requirement that the inner core boundary be observable by seismological means and the freezing behavior of solutions leads to the possibility that the outer core may contain a significant fraction of solid material. It is found that convection in the outer core is not hindered if the solid particles are entrained in the fluid flow. This model for a core of Fe and S admits temperatures in the range 3450K to 4200K at the top of the core. An all liquid Fe-S outer core would require a temperature of about 4900 K at the top of the core.

Part II.

The abundance of uses for organic compounds in the modern world results in many applications in which these materials are subjected to high pressures. This leads to the desire to be able to describe the behavior of these materials under such conditions. Unfortunately, the number of compounds is much greater than the number of experimental data available for many of the important properties. In the past, one approach that has worked well is the calculation of appropriate properties by summing the contributions from the organic functional groups making up molecules of the compounds in question. A new set of group contributions for the molar volume, volume thermal expansivity, heat capacity, and the Rao function is presented for functional groups containing C, H, and O. This set is, in most cases, limited in application to low molecular liquids. A new technique for the calculation of the pressure derivative of the bulk modulus is also presented. Comparison with data indicates that the presented technique works very well for most low molecular hydrocarbon liquids and somewhat less well for oxygen-bearing compounds. A similar comparison of previous results for polymers indicates that the existing tabulations of group contributions for this class of materials is in need of revision. There is also evidence that the Rao function contributions for polymers and low molecular compounds are somewhat different.

A model for energy and morphology of crystalline grain boundaries with arbitrary geometric character

It has been well-established that interfaces in crystalline materials are key players in the mechanics of a variety of mesoscopic processes such as solidification, recrystallization, grain boundary migration, and severe plastic deformation. In particular, interfaces with complex morphologies have been observed to play a crucial role in many micromechanical phenomena such as grain boundary migration, stability, and twinning. Interfaces are a unique type of material defect in that they demonstrate a breadth of behavior and characteristics eluding simplified descriptions. Indeed, modeling the complex and diverse behavior of interfaces is still an active area of research, and to the author's knowledge there are as yet no predictive models for the energy and morphology of interfaces with arbitrary character. The aim of this thesis is to develop a novel model for interface energy and morphology that i) provides accurate results (especially regarding "energy cusp" locations) for interfaces with arbitrary character, ii) depends on a small set of material parameters, and iii) is fast enough to incorporate into large scale simulations.

In the first half of the work, a model for planar, immiscible grain boundary is formulated. By building on the assumption that anisotropic grain boundary energetics are dominated by geometry and crystallography, a construction on lattice density functions (referred to as "covariance") is introduced that provides a geometric measure of the order of an interface. Covariance forms the basis for a fully general model of the energy of a planar interface, and it is demonstrated by comparison with a wide selection of molecular dynamics energy data for FCC and BCC tilt and twist boundaries that the model accurately reproduces the energy landscape using only three material parameters. It is observed that the planar constraint on the model is, in some cases, over-restrictive; this motivates an extension of the model.

In the second half of the work, the theory of faceting in interfaces is developed and applied to the planar interface model for grain boundaries. Building on previous work in mathematics and materials science, an algorithm is formulated that returns the minimal possible energy attainable by relaxation and the corresponding relaxed morphology for a given planar energy model. It is shown that the relaxation significantly improves the energy results of the planar covariance model for FCC and BCC tilt and twist boundaries. The ability of the model to accurately predict faceting patterns is demonstrated by comparison to molecular dynamics energy data and experimental morphological observation for asymmetric tilt grain boundaries. It is also demonstrated that by varying the temperature in the planar covariance model, it is possible to reproduce a priori the experimentally observed effects of temperature on facet formation.

Finally, the range and scope of the covariance and relaxation models, having been demonstrated by means of extensive MD and experimental comparison, future applications and implementations of the model are explored.

SteelConverter and Caltech VirtualShaker: Rapid Nonlinear Cloud-Based Structural Model Conversion and Analysis

STEEL, the Caltech created nonlinear large displacement analysis software, is currently used by a large number of researchers at Caltech. However, due to its complexity, lack of visualization tools (such as pre- and post-processing capabilities) rapid creation and analysis of models using this software was difficult. SteelConverter was created as a means to facilitate model creation through the use of the industry standard finite element solver ETABS. This software allows users to create models in ETABS and intelligently convert model information such as geometry, loading, releases, fixity, etc., into a format that STEEL understands. Models that would take several days to create and verify now take several hours or less. The productivity of the researcher as well as the level of confidence in the model being analyzed is greatly increased.

It has always been a major goal of Caltech to spread the knowledge created here to other universities. However, due to the complexity of STEEL it was difficult for researchers or engineers from other universities to conduct analyses. While SteelConverter did help researchers at Caltech improve their research, sending SteelConverter and its documentation to other universities was less than ideal. Issues of version control, individual computer requirements, and the difficulty of releasing updates made a more centralized solution preferred. This is where the idea for Caltech VirtualShaker was born. Through the creation of a centralized website where users could log in, submit, analyze, and process models in the cloud, all of the major concerns associated with the utilization of SteelConverter were eliminated. Caltech VirtualShaker allows users to create profiles where defaults associated with their most commonly run models are saved, and allows them to submit multiple jobs to an online virtual server to be analyzed and post-processed. The creation of this website not only allowed for more rapid distribution of this tool, but also created a means for engineers and researchers with no access to powerful computer clusters to run computationally intensive analyses without the excessive cost of building and maintaining a computer cluster.

In order to increase confidence in the use of STEEL as an analysis system, as well as verify the conversion tools, a series of comparisons were done between STEEL and ETABS. Six models of increasing complexity, ranging from a cantilever column to a twenty-story moment frame, were analyzed to determine the ability of STEEL to accurately calculate basic model properties such as elastic stiffness and damping through a free vibration analysis as well as more complex structural properties such as overall structural capacity through a pushover analysis. These analyses showed a very strong agreement between the two softwares on every aspect of each analysis. However, these analyses also showed the ability of the STEEL analysis algorithm to converge at significantly larger drifts than ETABS when using the more computationally expensive and structurally realistic fiber hinges. Following the ETABS analysis, it was decided to repeat the comparisons in a software more capable of conducting highly nonlinear analysis, called Perform. These analyses again showed a very strong agreement between the two softwares in every aspect of each analysis through instability. However, due to some limitations in Perform, free vibration analyses for the three story one bay chevron brace frame, two bay chevron brace frame, and twenty story moment frame could not be conducted. With the current trend towards ultimate capacity analysis, the ability to use fiber based models allows engineers to gain a better understanding of a building’s behavior under these extreme load scenarios.

Following this, a final study was done on Hall’s U20 structure [1] where the structure was analyzed in all three softwares and their results compared. The pushover curves from each software were compared and the differences caused by variations in software implementation explained. From this, conclusions can be drawn on the effectiveness of each analysis tool when attempting to analyze structures through the point of geometric instability. The analyses show that while ETABS was capable of accurately determining the elastic stiffness of the model, following the onset of inelastic behavior the analysis tool failed to converge. However, for the small number of time steps the ETABS analysis was converging, its results exactly matched those of STEEL, leading to the conclusion that ETABS is not an appropriate analysis package for analyzing a structure through the point of collapse when using fiber elements throughout the model. The analyses also showed that while Perform was capable of calculating the response of the structure accurately, restrictions in the material model resulted in a pushover curve that did not match that of STEEL exactly, particularly post collapse. However, such problems could be alleviated by choosing a more simplistic material model.

Photochemical electron transfer at fixed distance : a synthetic model of the photosynthetic primary process

A series of meso-phenyloctamethylporphyrins covalently bonded at the 4'phenyl position to quinones via rigid bicyclo[2.2.2]octane spacers were synthesized for the study of the dependence of electron transfer reaction rate on solvent, distance, temperature, and energy gap. A general and convergent synthesis was developed based on the condensation of ac-biladienes with masked quinonespacer-benzaldehydes. From picosecond fluorescence spectroscopy emission lifetimes were measured in seven solvents of varying polarity. Rate constants were determined to vary from 5.0x10⁹sec^-1 in N,N-dimethylformamide to 1.15x10¹⁰ Sec^-1 in benzene, and were observed to rise at most by about a factor of three with decreasing solvent polarity. Experiments at low temperature in 2-MTHF glass (77K) revealed fast, nearly temperature-independent electron transfer characterized by non-exponential fluorescence decays, in contrast to monophasic behavior in fluid solution at 298K. This example evidently represents the first photosynthetic model system not based on proteins to display nearly temperature-independent electron transfer at high temperatures (nuclear tunneling). Low temperatures appear to freeze out the rotational motion of the chromophores, and the observed nonexponential fluorescence decays may be explained as a result of electron transfer from an ensemble of rotational conformations. The nonexponentiality demonstrates the sensitivity of the electron transfer rate to the precise magnitude of the electronic matrix element, which supports the expectation that electron transfer is nonadiabatic in this system. The addition of a second bicyclooctane moiety (15 Å vs. 18 Å edge-to-edge between porphyrin and quinone) reduces the transfer rate by at least a factor of 500-1500. Porphyrinquinones with variously substituted quinones allowed an examination of the dependence of the electron transfer rate constant κ_ET on reaction driving force. The classical trend of increasing rate versus increasing exothermicity occurs from 0.7 eV≤ |ΔG^0'(R)| ≤ 1.0 eV until a maximum is reached (κ_ET = 3 x 10⁸ sec^-1 rising to 1.15 x 10¹⁰ sec^-1 in acetonitrile). The rate remains insensitive to ΔG⁰ for ~ 300 mV from 1.0 eV≤ |ΔG^0’(R)| ≤ 1.3 eV, and then slightly decreases in the most exothermic case studied (cyanoquinone, κ_ET = 5 x 10⁹ sec^-1).