Automated voltammetric system for shipboard determination of metal speciation in sea water

An automated and semi-intelligent voltammetric system is described for trace metal analysis. The system consists of a voltammeter interfaced with a personal computer, a sample changer, 2 peristaltic pumps, a motor burette and a hanging mercury drop electrode. The system carries out fully automatically approximately 5 metal determinations per hour (including at least 3 repetitive scans and calibration by standard addition) at trace levels encountered in clean sea water. The computer program decides what level of standard addition to use and evaluates the data prior to switching to the next sample. Alternatively, the system can be used to carry out complexing ligand titration with copper whilst recording the labile copper concentration; in this mode up to 8 full titrations are carried out per day. Depth profiles for chromium speciation in the Mediterranean Sea and a profile for copper complexing ligand concentrations in the North Atlantic Ocean measured on board-ship with the system are presented. The chromium speciation was determined using a new method to differentiate between Cr(III) and Cr(VI) utilizing adsorption of Cr(III) on silica particles.

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

DNA fingerprinting of selected Laminaria (Phaeophyta) gametophytes by RAPD markers

Random amplified polymorphism DNA (RAPD) analysis was applied to germplasm characterization in 33 different selected Laminaria male and female gametophytes. The positional homology of the RAPD analysis using sequence characterized applied region (SCAR) method was successfully conducted. A total of 233 polymorphic loci were obtained from 18 selected primers after screening, of which 27 stable and clear bands were selected to construct a fingerprint map for discrimination of each gametophyte. Seven RAPD markers from five primers were finally determined by a computer program to construct the fingerprint map. Three specific markers closely related with gametophytes were obtained and were converted to gametophytic SCAR markers, the first SCAR marker report on Laminaria germplasm and applicable to cultivars identification. These results demonstrated the feasibility of applying RAPD markers to germplasm characterization in selected Laminaria gametophytes, and can provide a molecular basis for breeding new Laminaria strains. (C) 2004 Elsevier B.V. All rights reserved.

Descriptive Simulation: Combining Symbolic and Numerical Methods in the Analysis of Chemical Reaction Mechanisms

The Kineticist's Workbench is a computer program currently under development whose purpose is to help chemists understand, analyze, and simplify complex chemical reaction mechanisms. This paper discusses one module of the program that numerically simulates mechanisms and constructs qualitative descriptions of the simulation results. These descriptions are given in terms that are meaningful to the working chemist (e.g., steady states, stable oscillations, and so on); and the descriptions (as well as the data structures used to construct them) are accessible as input to other programs.

The Bifurcation Interpreter: A Step Towards the Automatic Analysis of Dynamical Systems

The Bifurcation Interpreter is a computer program that autonomously explores the steady-state orbits of one-parameter families of periodically- driven oscillators. To report its findings, the Interpreter generates schematic diagrams and English text descriptions similar to those appearing in the science and engineering research literature. Given a system of equations as input, the Interpreter uses symbolic algebra to automatically generate numerical procedures that simulate the system. The Interpreter incorporates knowledge about dynamical systems theory, which it uses to guide the simulations, to interpret the results, and to minimize the effects of numerical error.

Sparse Representations for Fast, One-Shot Learning

Humans rapidly and reliably learn many kinds of regularities and generalizations. We propose a novel model of fast learning that exploits the properties of sparse representations and the constraints imposed by a plausible hardware mechanism. To demonstrate our approach we describe a computational model of acquisition in the domain of morphophonology. We encapsulate phonological information as bidirectional boolean constraint relations operating on the classical linguistic representations of speech sounds in term of distinctive features. The performance model is described as a hardware mechanism that incrementally enforces the constraints. Phonological behavior arises from the action of this mechanism. Constraints are induced from a corpus of common English nouns and verbs. The induction algorithm compiles the corpus into increasingly sophisticated constraints. The algorithm yields one-shot learning from a few examples. Our model has been implemented as a computer program. The program exhibits phonological behavior similar to that of young children. As a bonus the constraints that are acquired can be interpreted as classical linguistic rules.

Naive Physics, Event Perception, Lexical Semantics, and Language Acquisition

This thesis proposes a computational model of how children may come to learn the meanings of words in their native language. The proposed model is divided into two separate components. One component produces semantic descriptions of visually observed events while the other correlates those descriptions with co-occurring descriptions of those events in natural language. The first part of this thesis describes three implementations of the correlation process whereby representations of the meanings of whole utterances can be decomposed into fragments assigned as representations of the meanings of individual words. The second part of this thesis describes an implemented computer program that recognizes the occurrence of simple spatial motion events in simulated video input.

Automatic Qualitative Modeling of Dynamic Physical Systems

This report describes MM, a computer program that can model a variety of mechanical and fluid systems. Given a system's structure and qualitative behavior, MM searches for models using an energy-based modeling framework. MM uses general facts about physical systems to relate behavioral and model properties. These facts enable a more focussed search for models than would be obtained by mere comparison of desired and predicted behaviors. When these facts do not apply, MM uses behavior-constrained qualitative simulation to verify candidate models efficiently. MM can also design experiments to distinguish among multiple candidate models.

Toward a Theory of Representation Design

This research is concerned with designing representations for analytical reasoning problems (of the sort found on the GRE and LSAT). These problems test the ability to draw logical conclusions. A computer program was developed that takes as input a straightforward predicate calculus translation of a problem, requests additional information if necessary, decides what to represent and how, designs representations capturing the constraints of the problem, and creates and executes a LISP program that uses those representations to produce a solution. Even though these problems are typically difficult for theorem provers to solve, the LISP program that uses the designed representations is very efficient.

Qualitative Process Theory

Objects move, collide, flow, bend, heat up, cool down, stretch, compress and boil. These and other things that cause changes in objects over time are intuitively characterized as processes. To understand common sense physical reasoning and make programs that interact with the physical world as well as people do we must understand qualitative reasoning about processes, when they will occur, their effects, and when they will stop. Qualitative Process theory defines a simple notion of physical process that appears useful as a language in which to write dynamical theories. Reasoning about processes also motivates a new qualitative representation for quantity in terms of inequalities, called quantity space. This report describes the basic concepts of Qualitative Process theory, several different kinds of reasoning that can be performed with them, and discusses its impact on other issues in common sense reasoning about the physical world, such as causal reasoning and measurement interpretation. Several extended examples illustrate the utility of the theory, including figuring out that a boiler can blow up, that an oscillator with friction will eventually stop, and how to say that you can pull with a string but not push with it. This report also describes GIZMO, an implemented computer program which uses Qualitative Process theory to make predictions and interpret simple measurements. The represnetations and algorithms used in GIZMO are described in detail, and illustrated using several examples.

A Model for Deliberation, Action, and Introspection

This thesis investigates the problem of controlling or directing the reasoning and actions of a computer program. The basic approach explored is to view reasoning as a species of action, so that a program might apply its reasoning powers to the task of deciding what inferences to make as well as deciding what other actions to take. A design for the architecture of reasoning programs is proposed. This architecture involves self-consciousness, intentional actions, deliberate adaptations, and a form of decision-making based on dialectical argumentation. A program based on this architecture inspects itself, describes aspects of itself, and uses this self-reference and these self-descriptions in making decisions and taking actions. The program's mental life includes awareness of its own concepts, beliefs, desires, intentions, inferences, actions, and skills. All of these are represented by self-descriptions in a single sort of language, so that the program has access to all of these aspects of itself, and can reason about them in the same terms.

Symbolic Mathematical Laboratory

A large computer program has been developed to aid applied mathematicians in the solution of problems in non-numerical analysis which involve tedious manipulations of mathematical expressions. The mathematician uses typed commands and a light pen to direct the computer in the application of mathematical transformations; the intermediate results are displayed in standard text-book format so that the system user can decide the next step in the problem solution. Three problems selected from the literature have been solved to illustrate the use of the system. A detailed analysis of the problems of input, transformation, and display of mathematical expressions is also presented.

A Planning System for Robot Construction Tasks

This paper describes BUILD, a computer program which generates plans for building specified structures out of simple objects such as toy blocks. A powerful heuristic control structure enables BUILD to use a number of sophisticated construction techniques in its plans. Among these are the incorporation of pre-existing structure into the final design, pre-assembly of movable sub-structures on the table, and use of the extra blocks as temporary supports and counterweights in the course of construction. BUILD does its planning in a modeled 3-space in which blocks of various shapes and sizes can be represented in any orientation and location. The modeling system can maintain several world models at once, and contains modules for displaying states, testing them for inter-object contact and collision, and for checking the stability of complex structures involving frictional forces. Various alternative approaches are discussed, and suggestions are included for the extension of BUILD-like systems to other domains. Also discussed are the merits of BUILD's implementation language, CONNIVER, for this type of problem solving.

Causal and Teleological Reasoning in Circuit Recognition

This thesis presents a theory of human-like reasoning in the general domain of designed physical systems, and in particular, electronic circuits. One aspect of the theory, causal analysis, describes how the behavior of individual components can be combined to explain the behavior of composite systems. Another aspect of the theory, teleological analysis, describes how the notion that the system has a purpose can be used to aid this causal analysis. The theory is implemented as a computer program, which, given a circuit topology, can construct by qualitative causal analysis a mechanism graph describing the functional topology of the system. This functional topology is then parsed by a grammar for common circuit functions. Ambiguities are introduced into the analysis by the approximate qualitative nature of the analysis. For example, there are often several possible mechanisms which might describe the circuit's function. These are disambiguated by teleological analysis. The requirement that each component be assigned an appropriate purpose in the functional topology imposes a severe constraint which eliminates all the ambiguities. Since both analyses are based on heuristics, the chosen mechanism is a rationalization of how the circuit functions, and does not guarantee that the circuit actually does function. This type of coarse understanding of circuits is useful for analysis, design and troubleshooting.

The structure of nano sized poorly-crystalline iron oxy-hydroxides

In this thesis the structures of three nano sized poorly-crystalline iron oxy-hydroxides, feroxyhyte, ferrihydrite and schwertmannite, are studied and analyzed with the aim of clarifying some dubious structural features. The widely used Rietveld re�nement and EXAFS analysis are employed in order to address the consistency of the structural models proposed for these materials, one of which, feroxyhyte, is suggested in this thesis. Furthermore, a new computer program exploiting the Reverse Monte Carlo algorithm and the Debye Scattering Equation is presented and used in order to analyze the elusive structures of these iron oxy-hydroxides.