Two essays in computational optimization: computing the clar number in fullerene graphs and distributing the errors in iterative interior point methods

Fullerene are cage-like hollow carbon molecules graph of pseudospherical sym- metry consisting of only pentagons and hexagons faces. It has been the object of interest for chemists and mathematicians due to its widespread application in various fields, namely including electronic and optic engineering, medical sci- ence and biotechnology. A Fullerene molecular, Γ n of n atoms has a multiplicity of isomers which increases as N iso ∼ O(n 9 ). For instance, Γ 180 has 79,538,751 isomers. The Fries and Clar numbers are stability predictors of a Fullerene molecule. These number can be computed by solving a (possibly N P -hard) combinatorial optimization problem. We propose several ILP formulation of such a problem each yielding a solution algorithm that provides the exact value of the Fries and Clar numbers. We compare the performances of the algorithm derived from the proposed ILP formulations. One of this algorithm is used to find the Clar isomers, i.e., those for which the Clar number is maximum among all isomers having a given size. We repeated this computational experiment for all sizes up to 204 atoms. In the course of the study a total of 2 649 413 774 isomers were analyzed.The second essay concerns developing an iterative primal dual infeasible path following (PDIPF) interior point (IP) algorithm for separable convex quadratic minimum cost flow network problem. In each iteration of PDIPF algorithm, the main computational effort is solving the underlying Newton search direction system. We concentrated on finding the solution of the corresponding linear system iteratively and inexactly. We assumed that all the involved inequalities can be solved inexactly and to this purpose, we focused on different approaches for distributing the error generated by iterative linear solvers such that the convergences of the PDIPF algorithm are guaranteed. As a result, we achieved theoretical bases that open the path to further interesting practical investiga- tion

Estimation method for the thermochemical properties of polycyclic aromatic molecules

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005.Includes bibliographical references.Polycyclic aromatic molecules, including polycyclic aromatic hydrocarbons (PAHs) have attracted considerable attention in the past few decades. They are formed during the incomplete combustion of hydrocarbon fuels and are precursors of soot. Some PAHs are known carcinogens, and control of their emissions is an important issue. These molecules are found in many materials, including coal, fuel oils, lubricants, and carbon black. They are also implicated in the formation of fullerenes, one of the most. chemically versatile class of molecules known. Clearly, models that provide predictive capability for their formation and growth are highly desirable. Thlermochemical properties of the species in the model are often the most important parameter, particularly for high temperature processes such as the formation of PAH and other aromatic molecules. Thermodynamic consistency requires that reverse rate constants be calculated from the forward rate constants and from the equilibrium constants. The later are obtained from the thermochemical properties of reactants and products. The predictive ability of current kinetic models is significantly limited by the scarcity of available thermochemical data.(cont.) In this work we present the development of a Bond-Centered Group Additivity method for the estimation of the thermochemical properties of polycyclic aromatic molecules, including PAHs, molecules with the furan substructure, molecules with triple bonds, substituted PAHs, and radicals. This method is based on thermochemical values of about two hundred polycyclic aromatic molecules and radicals obtained from quantum chemical calculations at the B3LYP/6-31G(d) level. A consistent set of homodesmic reactions has been developed to accurately calculate the heat of formation from the absolute energy. The entropies calculated from the B3LYP/6-31G(d) vibrational frequencies are shown to be at least as reliable as the few available experimental values. This new Bond-Centered Group Additivity method predicts the thermochemistry of C₆₀ and C₇₀ fullerenes, as well as smaller aromatic molecules, with accuracy comparable to both experiments and the best quantum calculations. This Bond-Centered Group Additivity method is shown to extrapolate reasonably to infinite graphene sheets.(cont.) The Bond-Centered Group Additivity method has been implemented into a computer code within the automatic Reaction Mechanism Generation software (RMG) developed in our group. The database has been organized as a tree structure, making its maintenance and possible extension very straightforward. This computer code allows the fast and easy use of this estimation method by non-expert users. Moreover, since it is incorporated into RMG, it will allow users to generate reaction mechanisms that include aromatic molecules whose thermochemical properties are calculated using the Bond-Centered Group Additivity method. Exploratory equilibrium studies were performed (l. Equilibrium concentrations of individual species depend strongly on the thermochemistry of the individual species, emphasizing the importance of consistent thermochemistry for all the species involved in the calculations. Equilibrium calculations can provide many interesting insights into the relationship between PAH and fullerenes in combustion.by Joanna Yu.Ph.D

Gas sensing using an organic/silicon hybrid field-effect transistor

This thesis describes the fabrication and properties of novel organic/silicon hybrid field-effect transistor gas sensors. Whilst most of the work used the emeraldine base form of the conductive polymer polyaniline, the response of a device incorporating a metal-free phthalocyanine is also reported. Arrays of p-type transistors in which the gate electrodes were replaced by 'charge-flow' capacitors were fabricated using standard semiconductor processing techniques. Each array consisted of four devices in which the width of metallisation removed from the gate electrode (total width 72 µm) varied from 0 µm (i.e. the control device) to 35 µm. Thin films of the gas-sensitive organic materials were deposited by spin-coating, and chemically patterned within the holes in the gate metallisation. A delay, referred to as the 'turn-on' response, was observed in the drain current on application of a gate voltage. This was shown to depend on the temperature, level of humidity and the presence of certain gases. The electrical operating characteristics of the hybrid device with and without the polyaniline were examined. These included capacitance-voltage measurements, the 'turn-on' response at different temperatures and the variation of threshold voltage with temperature. From these results an understanding of the effect of integrating polyaniline within a p-channel transistor structure was obtained. The 35 µm gate-hole sensor incorporating polyaniline was found to be sensitive to NO(_x) and SO(_2) at room temperature at concentrations as low as 1 or 2 ppm. Decreasing the gate-hole area, and therefore the surface area of polyaniline, reduced the sensitivity of the device. The reactions were found to be reversible, although complete recovery required approximately eight hours. A similar sensor incorporating a metal-free phthalocyanine compound was reversibly sensitive to 2 ppm NO(_x) with a more rapid recovery of five hours. There was no observable response to SO(_2) or H(_2)S up to 30 ppm

Çok parçacıklı sistemlerin geometri optimizasyonu için parelel kod geliştirilmesi: nano-sistemlerde hidrojen depolama ve nano ölçekli mıknatıs yapılarının incelenmesi uygulamaları

TÜBİTAK TBAG Proje01.07.200

Advances in Plasma Processes for Polymers

Polymerized nanoparticles and nanofibers can be prepared using various processes, such as chemical synthesis, the electrochemical method, electrospinning, ultrasonic irradiation, hard and soft templates, seeding polymerization, interfacial polymerization, and plasma polymerization. Among these processes, plasma polymerization and aerosol-through-plasma (A-T-P) processes have versatile advantages, especially due to them being “dry", for the deposition of plasma polymer films and carbon-based materials with functional properties suitable for a wide range of applications, such as electronic and optical devices, protective coatings, and biomedical materials. Furthermore, it is well known that plasma polymers are highly cross-linked, pinhole free, branched, insoluble, and adhere well to most substrates. In order to synthesize the polymer films using the plasma processes, therefore, it is very important to increase the density and electron temperature of plasma during plasma polymerization

Algorithms for the count of linearly independent and minimal conjugated circuits in benzenoid hydrocarbons

Available forms of the minimal conjugated circuits for any ring s in a Kekule structure are studied, and appropriate algorithms are found to adapt the different cases. On the basis of these algorithms, a direct method for the calculation of the summation expression of linearly independent and minimal conjugated circuits in benzenoid hydrocarbons is proposed, and it is realized within software on a PC

Technology 2001: The Second National Technology Transfer Conference and Exposition, volume 1

Papers from the technical sessions of the Technology 2001 Conference and Exposition are presented. The technical sessions featured discussions of advanced manufacturing, artificial intelligence, biotechnology, computer graphics and simulation, communications, data and information management, electronics, electro-optics, environmental technology, life sciences, materials science, medical advances, robotics, software engineering, and test and measurement

The 1st International Electronic Conference on Chemical Sensors and Analytical Chemistry

The 1st International Electronic Conference on Chemical Sensors and Analytical Chemistry was held on 1–15 July 2021. The scope of this online conference was to gather experts that are well-known worldwide who are currently working in chemical sensor technologies and to provide an online forum for the presention and discussion of new results. Throughout this event, topics of interest included, but were not limited to, the following: electrochemical devices and sensors; optical chemical sensors; mass-sensitive sensors; materials for chemical sensing; nano- and micro-technologies for sensing; chemical assays and validation; chemical sensor applications; analytical methods; gas sensors and apparatuses; electronic noses; electronic tongues; microfluidic devices; lab-on-a-chip; single-molecule sensing; nanosensors; and medico-diagnostic testing