Institute for Systems Research
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Item Synthesis of Direct Mechanisms for Chemical Systems(1991) Mavrovouniotis, Micheal L.; ISRA chemical system consists of intermediate species, terminal species, and mechanism steps. Understanding the behavior of a chemical system can be significantly aided by the identification of mechanisms responsible for overall reactions which do not involve net consumption or production of reaction intermediates. Issues arising in the definition and identification of direct mechanisms, which are the shortest possible mechanisms, are discussed. In the context of examples of catalytic synthesis of ammonia and methanol, an alternative approach for the construction of mechanisms from steps is presented. An algorithm for the construction of direct mechanisms is then formally stated; the algorithm is based on successive processing and elimination of reaction intermediates which should not appear in the overall stoichiometry of the reactions accomplished by the mechanisms. Throughout the operation of the algorithm, irreversible steps are used only in their permitted direction. The basic algorithm may construct indirect or duplicate mechanisms, but variations of the algorithm are proposed which discard such redundant mechanisms. A number of hypothetical chemical systems illustrate the differences between the proposed algorithm and other approaches.Item Computer-Manipulation of Conjugate Forms in Proper Estimation(1991) Mavrovouniotis, Micheal L.; Constantinou, Leonidas A.; ISRPhysical and chemical properties of pure compounds and mixtures are essential for the analysis and design of chemical processing systems. A method for the estimation of properties of organic compounds from their molecular structure is presented, based on the contributions of Atoms and Bonds in the properties of Conjugate forms of a molecular structure (ABC). A real chemical compound can be considered the hybrid of a number of conjugates, which are alternative formal arrangements of the valence electrons of the molecule. The property-estimation method generates all conjugate forms of the molecule and assigns properties to each conjugate, simply by summing contributions from atoms and bonds in the particular electronic arrangement of the conjugate. The properties of the actual compound are then derived from the properties of the conjugates. The generation and analysis of conjugates is based on symbolic computation and Object-Oriented Programming (OOP). Atoms, bonds, molecules, electron pairs, and other entities can be represented as interconnected objects within OOP. The generation, comparison, and analysis of conjugates can be carried out through computer- based manipulation of the objects and their interconnections. One needs to encode operators which generate the conjugates, as well a rules for pruning the generation so that only the most important conjugates are considered. The nature and connectivity of atoms within a molecule determine the physical and chemical properties of the molecule. Traditional group-contribution methods eliminate much of the detailed molecular-structure information at an early stage of the property-estimation effort. Through symbolic computation and the concept of conjugation, the ABC approach aims to use molecular structure information more effectively.Item Hierarchical Neural Networks(1991) Mavrovouniotis, Micheal L.; ISRWith the common three-layer neural network architectures, networks lack internal structure; as a consequence, it is very difficult to discern characteristics of the knowledge acquired by a network, in order to evaluate its reliability and applicability. An alternative neural-network architecture is presented, based on a hierarchical organization. Hierarchical networks consist of a number of loosely-coupled subnets, arranged in layers. Each subnet is intended to capture specific aspects of the input data. A subnet models a particular subset of the input variables, but the exact patterns and relationships among variables are determined by training the network as a whole. However, the hierarchy of subnets gives the network hints to look for patterns in the most promising directions. Their modular organization makes hierarchical neural networks easier to analyze, because one can focus on the analysis of one subnet at a time, rather than attempt to decipher the whole network at once.Item Vector Notation for Partial Molar Properties in Single-Phase Simple Systems(1990) Mavrovouniotis, Micheal L.; ISRConventional coordinate systems used in thermodynamic analysis of mixtures use either mole numbers or mole fractions as independent variables. The definition of quantities and the derivation of relationships in these systems entail formidable algebra. The introduction of a position vector for the amount and composition of a multi-component mixture allows the expression of useful derivative quantities in vector and tensor notation, independently of the coordinate system used.Item Estimation of Properties from Conjugate Forms of Molecular Structures: The ABC Approach(1990) Mavrovouniotis, Micheal L.; ISRThe ABC technique for estimating properties of organic compounds from their molecular structures is presented, based on the contributions of Atoms and Bonds to the properties of Conjugates. Conjugates are alternative formal arrangements of valence electrons; a real chemical compound is a hybrid of conjugates. In ABC conjugates of a molecule are generated, and thermodynamic and quantummechanical properties are assigned to each conjugate, by summing contributions from atoms and bonds of the conjugate; the properties of the compound are then obtained as combinations of the properties of all the conjugates. In a simple application, ABC estimates the heat of formation of alkanes within 2.8kJ/mol, compared to 4.7kJ/mol for group contributions. The ultimate goal is the estimation of fractional charges on individual atoms of a compound and electron densities of bonds, because these are related to intermolecular interactions and chemical properties.Item Computer-Aided Synthesis of Biochemical Pathways(1990) Mavrovouniotis, Micheal L.; ISRThe synthesis of biochemical pathways satisfying stoichiometric constraints is discussed. Stoichiometric constraints arise primarily from designating compounds as required or allowed reactants, and required or allowed products of the pathways; they also arise from similar restrictions on intermediate metabolites and bioreactions participating in the pathways. An algorithm for the complete and correct solution of the problem is presented; the algorithm satisfies each constraint by recursively transforming a base-set of pathways. The algorithm is applied to the problem of lysine synthesis from glucose and ammonia. In addition to the established synthesis routes, the algorithm constructs several alternative pathways that bypass key enzymes, such as malate dehydrogenase and pyruvate dehydrogenase. Apart from the construction of pathways with desired characteristics, the systematic synthesis of pathways can also uncover fundamental constraints in a particular problem, by demonstrating that no pathways exist to meet certain sets of specifications. In the case of lysine, the algorithm shows that oxaloacetate is a necessary intermediate in all pathways leading to lysine from glucose, and that the yield of lysine over glucose cannot exceet 67% in the absence of enzymatic recovery of carbon dioxide.