Modeling, Estimation, and Control of Robot-Soil Interactions

This thesis presents the development of hardware, theory, and experimental methods to enable a robotic manipulator arm to interact with soils and estimate soil properties from interaction forces. Unlike the majority of robotic systems interacting with soil, our objective is parameter estimation, not excavation. To this end, we design our manipulator with a flat plate for easy modeling of interactions. By using a flat plate, we take advantage of the wealth of research on the similar problem of earth pressure on retaining walls. There are a number of existing earth pressure models. These models typically provide estimates of force which are in uncertain relation to the true force. A recent technique, known as numerical limit analysis, provides upper and lower bounds on the true force. Predictions from the numerical limit analysis technique are shown to be in good agreement with other accepted models. Experimental methods for plate insertion, soil-tool interface friction estimation, and control of applied forces on the soil are presented. In addition, a novel graphical technique for inverting the soil models is developed, which is an improvement over standard nonlinear optimization. This graphical technique utilizes the uncertainties associated with each set of force measurements to obtain all possible parameters which could have produced the measured forces. The system is tested on three cohesionless soils, two in a loose state and one in a loose and dense state. The results are compared with friction angles obtained from direct shear tests. The results highlight a number of key points. Common assumptions are made in soil modeling. Most notably, the Mohr-Coulomb failure law and perfectly plastic behavior. In the direct shear tests, a marked dependence of friction angle on the normal stress at low stresses is found. This has ramifications for any study of friction done at low stresses. In addition, gradual failures are often observed for vertical tools and tools inclined away from the direction of motion. After accounting for the change in friction angle at low stresses, the results show good agreement with the direct shear values.

Understanding Subsystems in Biology through Dimensionality Reduction, Graph Partitioning and Analytical Modeling

Biological systems exhibit rich and complex behavior through the orchestrated interplay of a large array of components. It is hypothesized that separable subsystems with some degree of functional autonomy exist; deciphering their independent behavior and functionality would greatly facilitate understanding the system as a whole. Discovering and analyzing such subsystems are hence pivotal problems in the quest to gain a quantitative understanding of complex biological systems. In this work, using approaches from machine learning, physics and graph theory, methods for the identification and analysis of such subsystems were developed. A novel methodology, based on a recent machine learning algorithm known as non-negative matrix factorization (NMF), was developed to discover such subsystems in a set of large-scale gene expression data. This set of subsystems was then used to predict functional relationships between genes, and this approach was shown to score significantly higher than conventional methods when benchmarking them against existing databases. Moreover, a mathematical treatment was developed to treat simple network subsystems based only on their topology (independent of particular parameter values). Application to a problem of experimental interest demonstrated the need for extentions to the conventional model to fully explain the experimental data. Finally, the notion of a subsystem was evaluated from a topological perspective. A number of different protein networks were examined to analyze their topological properties with respect to separability, seeking to find separable subsystems. These networks were shown to exhibit separability in a nonintuitive fashion, while the separable subsystems were of strong biological significance. It was demonstrated that the separability property found was not due to incomplete or biased data, but is likely to reflect biological structure.

The Individual is Nothing, the Class Everything: Psychophysics and Modeling of Recognition in Obect Classes

Most psychophysical studies of object recognition have focussed on the recognition and representation of individual objects subjects had previously explicitely been trained on. Correspondingly, modeling studies have often employed a 'grandmother'-type representation where the objects to be recognized were represented by individual units. However, objects in the natural world are commonly members of a class containing a number of visually similar objects, such as faces, for which physiology studies have provided support for a representation based on a sparse population code, which permits generalization from the learned exemplars to novel objects of that class. In this paper, we present results from psychophysical and modeling studies intended to investigate object recognition in natural ('continuous') object classes. In two experiments, subjects were trained to perform subordinate level discrimination in a continuous object class - images of computer-rendered cars - created using a 3D morphing system. By comparing the recognition performance of trained and untrained subjects we could estimate the effects of viewpoint-specific training and infer properties of the object class-specific representation learned as a result of training. We then compared the experimental findings to simulations, building on our recently presented HMAX model of object recognition in cortex, to investigate the computational properties of a population-based object class representation as outlined above. We find experimental evidence, supported by modeling results, that training builds a viewpoint- and class-specific representation that supplements a pre-existing repre-sentation with lower shape discriminability but possibly greater viewpoint invariance.

On the difficulty of feature-based attentional modulations in visual object recognition: A modeling study.

Numerous psychophysical experiments have shown an important role for attentional modulations in vision. Behaviorally, allocation of attention can improve performance in object detection and recognition tasks. At the neural level, attention increases firing rates of neurons in visual cortex whose preferred stimulus is currently attended to. However, it is not yet known how these two phenomena are linked, i.e., how the visual system could be "tuned" in a task-dependent fashion to improve task performance. To answer this question, we performed simulations with the HMAX model of object recognition in cortex [45]. We modulated firing rates of model neurons in accordance with experimental results about effects of feature-based attention on single neurons and measured changes in the model's performance in a variety of object recognition tasks. It turned out that recognition performance could only be improved under very limited circumstances and that attentional influences on the process of object recognition per se tend to display a lack of specificity or raise false alarm rates. These observations lead us to postulate a new role for the observed attention-related neural response modulations.

On blame-freeness and reciprocity: an experimental study

The theory of reciprocity is predicated on the assumption that people are willing to reward nice or kind acts and to punish unkind ones. This assumption raises the question as to how to define kindness. In this paper we offer a new definition of kindness that we call “blame-freeness.” Put most simply, blame-freeness states that in judging whether player i has been kind or unkind to player j in a social situation, player j would have to put himself in the strategic position of player i, while retaining his preferences, and ask if he would have acted in a manner that was worse than i did under identical circumstances. If j would have acted in a more unkind manner than i acted, then we say that j does not blame i for his behavior. If, however, j would have been nicer than i was, then we say that “j blames i” for his actions (i’s actions were blameworthy). We consider this notion a natural, intuitive and empirically relevant way to explain the motives of people engaged in reciprocal behavior. After developing the conceptual framework, we then test this concept in a laboratory experiment involving tournaments and find significant support for the theory.

Modeling distributions of immediate memory effects: No strategies needed?

Many models of immediate memory predict the presence or absence of various effects, but none have been tested to see whether they predict an appropriate distribution of effect sizes. The authors show that the feature model (J. S. Nairne, 1990) produces appropriate distributions of effect sizes for both the phonological confusion effect and the word-length effect. The model produces the appropriate number of reversals, when participants are more accurate with similar items or long items, and also correctly predicts that participants performing less well overall demonstrate smaller and less reliable phonological similarity and word-length effects and are more likely to show reversals. These patterns appear within the model without the need to assume a change in encoding or rehearsal strategy or the deployment of a different storage buffer. The implications of these results and the wider applicability of the distributionmodeling approach are discussed.

Modeling chemotaxis reveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase

Understanding how multiple signals are integrated in living cells to produce a balanced response is a major challenge in biology. Two-component signal transduction pathways, such as bacterial chemotaxis, comprise histidine protein kinases (HPKs) and response regulators (RRs). These are used to sense and respond to changes in the environment. Rhodobacter sphaeroides has a complex chemosensory network with two signaling clusters, each containing a HPK, CheA. Here we demonstrate, using a mathematical model, how the outputs of the two signaling clusters may be integrated. We use our mathematical model supported by experimental data to predict that: (1) the main RR controlling flagellar rotation, CheY6, aided by its specific phosphatase, the bifunctional kinase CheA3, acts as a phosphate sink for the other RRs; and (2) a phosphorelay pathway involving CheB2 connects the cytoplasmic cluster kinase CheA3 with the polar localised kinase CheA2, and allows CheA3-P to phosphorylate non-cognate chemotaxis RRs. These two mechanisms enable the bifunctional kinase/phosphatase activity of CheA3 to integrate and tune the sensory output of each signaling cluster to produce a balanced response. The signal integration mechanisms identified here may be widely used by other bacteria, since like R. sphaeroides, over 50% of chemotactic bacteria have multiple cheA homologues and need to integrate signals from different sources.

First structural analysis of a naphthalene-based poly(ether ketone): Crystal and molecular simulation from X-ray powder data and diffraction modeling

Polycondensation of 2,6-dihydroxynaphthalene with 4,4'-bis(4"-fluorobenzoyl)biphenyl affords a novel, semicrystalline poly(ether ketone) with a melting point of 406 degreesC and glass transition temperature (onset) of 168 degreesC. Molecular modeling and diffraction-simulation studies of this polymer, coupled with data from the single-crystal structure of an oligomer model, have enabled the crystal and molecular structure of the polymer to be determined from X-ray powder data. This structure-the first for any naphthalene-containing poly(ether ketone)-is fully ordered, in monoclinic space group P2(1)/b, with two chains per unit cell. Rietveld refinement against the experimental powder data gave a final agreement factor (R-wp) of 6.7%.

Modeling the structure of amorphous MoS3: a neutron diffraction and reverse Monte Carlo study

A model for the structure of amorphous molybdenum trisulfide, a-MoS3, has been created using reverse Monte Carlo methods. This model, which consists of chains Of MoS6 units sharing three sulfurs with each of its two neighbors and forming alternate long, nonbonded, and short, bonded, Mo-Mo separations, is a good fit to the neutron diffraction data and is chemically and physically realistic. The paper identifies the limitations of previous models based on Mo-3 triangular clusters in accounting for the available experimental data.

Solid phases of cyclopentane: combined experimental and simulation study

The phase diagram of cyclopentane has been studied by powder neutron diffraction, providing diffraction patterns for phases I, II, and III, over a range of temperatures and pressures. The putative phase IV was not observed. The structure of the ordered phase III has been solved by single-crystal diffraction. Computational modeling reveals that there are many equienergetic ordered structures for cyclopentane within a small energy range. Molecular dynamics simulations reproduce the structures and diffraction patterns for phases I and III and also show an intermediate disordered phase, which is used to interpret phase II.

An experimental comparison between rival theories of rapid automatized naming performance and its relationship to reading

Two studies investigated the degree to which the relationship between rapid automatized naming (RAN) performance and reading development is driven by shared phonological processes. Study 1 assessed RAN, phonological awareness, and reading performance in 1010 7- to -10 year-olds. Results showed that RAN deficits occurred in the absence of phonological awareness deficits. These were accompanied by modest reading delays. In structural equation modeling, solutions where RAN was subsumed within a phonological processing factor did not provide a good fit to the data, suggesting that processes outside phonology may drive RAN performance and its association with reading. Study 2 investigated Kail’s proposal that speed of processing underlies this relationship. Children with single RAN deficits showed slower speed of processing than did closely matched controls performing normally on RAN. However, regression analysis revealed that RAN made a unique contribution to reading even after accounting for processing speed. Theoretical implications are discussed.

New mathematical modeling approach for predicting microbial inactivation by high hydrostatic pressure

A new primary model based on a thermodynamically consistent first-order kinetic approach was constructed to describe non-log-linear inactivation kinetics of pressure-treated bacteria. The model assumes a first-order process in which the specific inactivation rate changes inversely with the square root of time. The model gave reasonable fits to experimental data over six to seven orders of magnitude. It was also tested on 138 published data sets and provided good fits in about 70% of cases in which the shape of the curve followed the typical convex upward form. In the remainder of published examples, curves contained additional shoulder regions or extended tail regions. Curves with shoulders could be accommodated by including an additional time delay parameter and curves with tails shoulders could be accommodated by omitting points in the tail beyond the point at which survival levels remained more or less constant. The model parameters varied regularly with pressure, which may reflect a genuine mechanistic basis for the model. This property also allowed the calculation of (a) parameters analogous to the decimal reduction time D and z, the temperature increase needed to change the D value by a factor of 10, in thermal processing, and hence the processing conditions needed to attain a desired level of inactivation; and (b) the apparent thermodynamic volumes of activation associated with the lethal events. The hypothesis that inactivation rates changed as a function of the square root of time would be consistent with a diffusion-limited process.

Kinetic modeling of the generation of 2-and 3-methylbutanal in a heated extract of beef liver

Quantitative control of aroma generation during the Maillard reaction presents great scientific and industrial interest. Although there have been many studies conducted in simplified model systems, the results are difficult to apply to complex food systems, where the presence of other components can have a significant impact. In this work, an aqueous extract of defatted beef liver was chosen as a simplified food matrix for studying the kinetics of the Mallard reaction. Aliquots of the extract were heated under different time and temperature conditions and analyzed for sugars, amino acids, and methylbutanals, which are important Maillard-derived aroma compounds formed in cooked meat. Multiresponse kinetic modeling, based on a simplified mechanistic pathway, gave a good fit with the experimental data, but only when additional steps were introduced to take into account the interactions of glucose and glucose-derived intermediates with protein and other amino compounds. This emphasizes the significant role of the food matrix in controlling the Maillard reaction.

Development and experimental identification of a biomechanical model of the trunk for functional electrical stimulation control in paraplegia

Objectives. Theoretic modeling and experimental studies suggest that functional electrical stimulation (FES) can improve trunk balance in spinal cord injured subjects. This can have a positive impact on daily life, increasing the volume of bimanual workspace, improving sitting posture, and wheelchair propulsion. A closed loop controller for the stimulation is desirable, as it can potentially decrease muscle fatigue and offer better rejection to disturbances. This paper proposes a biomechanical model of the human trunk, and a procedure for its identification, to be used for the future development of FES controllers. The advantage over previous models resides in the simplicity of the solution proposed, which makes it possible to identify the model just before a stimulation session ( taking into account the variability of the muscle response to the FES). Materials and Methods. The structure of the model is based on previous research on FES and muscle physiology. Some details could not be inferred from previous studies, and were determined from experimental data. Experiments with a paraplegic volunteer were conducted in order to measure the moments exerted by the trunk-passive tissues and artificially stimulated muscles. Data for model identification and validation also were collected. Results. Using the proposed structure and identification procedure, the model could adequately reproduce the moments exerted during the experiments. The study reveals that the stimulated trunk extensors can exert maximal moment when the trunk is in the upright position. In contrast, previous studies show that able-bodied subjects can exert maximal trunk extension when flexed forward. Conclusions. The proposed model and identification procedure are a successful first step toward the development of a model-based controller for trunk FES. The model also gives information on the trunk in unique conditions, normally not observable in able-bodied subjects (ie, subject only to extensor muscles contraction).

Particle swarm optimization aided orthogonal forward regression for unified data modeling

We propose a unified data modeling approach that is equally applicable to supervised regression and classification applications, as well as to unsupervised probability density function estimation. A particle swarm optimization (PSO) aided orthogonal forward regression (OFR) algorithm based on leave-one-out (LOO) criteria is developed to construct parsimonious radial basis function (RBF) networks with tunable nodes. Each stage of the construction process determines the center vector and diagonal covariance matrix of one RBF node by minimizing the LOO statistics. For regression applications, the LOO criterion is chosen to be the LOO mean square error, while the LOO misclassification rate is adopted in two-class classification applications. By adopting the Parzen window estimate as the desired response, the unsupervised density estimation problem is transformed into a constrained regression problem. This PSO aided OFR algorithm for tunable-node RBF networks is capable of constructing very parsimonious RBF models that generalize well, and our analysis and experimental results demonstrate that the algorithm is computationally even simpler than the efficient regularization assisted orthogonal least square algorithm based on LOO criteria for selecting fixed-node RBF models. Another significant advantage of the proposed learning procedure is that it does not have learning hyperparameters that have to be tuned using costly cross validation. The effectiveness of the proposed PSO aided OFR construction procedure is illustrated using several examples taken from regression and classification, as well as density estimation applications.