Data Formats for Elementary Gas Phase Kinetics,Part 1: Unique Representations of Species at the Molecular Level

Standardized electronic formats for data are needed to efficiently and transparently communicate the results of scientific studies. A format for the unique identification of chemical species is a requirement in the field of chemistry, and the IUPAC International Chemical Identifier (InChI) has been widely adopted for this purpose. The InChI identifier has proved to be very useful. The InChI identifier, however, is currently insufficient to uniquely specify some types of molecular entities at a detailed molecular level needed to fully characterize their chemical nature, to differentiate between chemically distinct conformers, to uniquely identify structures used in quantum chemical calculations, and to completely describe elementary chemical reactions. To address this limitation, we propose an augmented form of InChI, denoted as InChI–ER, which contains additional optional layers that allow the unique and unambiguous identification of molecules at a detailed molecular level. The new layers proposed herein are optional extensions of the existing InChI formalism and, like all other InChI layers, would not interfere with InChI identifiers currently in use. The focus of the present work is the better specification of required molecular entities such as rotational conformations, ring conformations, and electronic states. In companion articles, we propose additional reaction layers using an extended InChI format that will enable the unique identification of elementary chemical reactions, including specification of associated transition states, specification of the changes in bonds that occur during reaction, and classification of reaction types.     

OPTIMAL CONTROL APPLIED TO RIFT VALLEY FEVER

Abstract Rift Valley Fever (RVF) virus is a mosquito‐born pathogen that infects livestock but it also has the capability to infect humans through direct or indirect contact with blood or organs of infected animals and by bites from infected mosquitos. The economic and social cost of the disease to rural populations can lead to a cascade of negative effects on the sustainability of animal and human populations. Vaccines exist to protect against this disease. Through a compartment model depicting the interactions leading to the spread of RVF in Aedes and Culex mosquitos and a livestock population, an optimal control problem is developed to minimize the number of vaccinated livestock at the final time while minimizing the negative effects of the infected Aedes and Culex mosquitos and the cost of the vaccination process. The unique optimal vaccination strategy is produced for given high transmission parameters and numerical results portray that vaccination depends on the level of effectiveness of the protocol.     

Acoustic Wave Propagation in an Underwater Sound Channel 2. Quantitative Theory

By using ray-theoretic-techniques we have developed in our previouspaper, "Acoustic Wave Propagation in an Underwater Sound Channel.1. Qualitative Theory" a certain qualitative understanding ofseveral features of SOFAR propagation in an underwater soundchannel. In the present paper a more penetrating quantitativestudy is done by means of analytical techniques on the governingequations. We study the transient problem for the Epstein profileby employing a double transform to formally derive an integralrepresentation, and we obtain several alternative representationsneeded for asymptotic results which we also present. It is believedthat several new and interesting asymptotic results have beenderived.     

Characterization of aromatic-thiol π-type hydrogen bonding and phenylalanine-cysteine side chain interactions through ab initio calculations and protein database analyses

In this study, the aromatic-thiol π hydrogen bonding and phenylalanine-cysteine side chain interactions are characterized through both molecular orbital calculations on a C₆H₆-HSCH₃ model complex and database analyses of 609 X-ray protein structures. The aromatic-thiol π hydrogen bonding interaction can achieve a stabilization energy of 2.60 kcal mol^?1, and is stronger than the already documented aromatic-hydroxyl and aromatic-amino hydrogen bonds. However, the occurrence of the aromatic-thiol hydrogen bond is rather rare in proteins. This is because most of the thiol groups participate in the formation of either disulphide bonds or stronger S—H…O (or N) ‘normal’ hydrogen bonds in a protein environment. Interactions between the side chains of phenylalanine and cysteine residues are characterized as the phenyl(Phe)(HSCH₂-)(Cys) interaction. The bonding energy for such interactions is approximately 3.71 kcal mol-¹ and is achieved in a geometric arrangement with an optimal phenyl(Phe)-(HS-)(Cys) π-type hydrogen bonding interaction. The interaction is very sensitive to the orientation of the two lone electron pairs on the sulphur atom relative to the π electron cloud of the phenyl ring. Accordingly, the interaction configurations that can accomplish a significant bonding energy exist only within a narrow configurational space. The database analysis of 609 experimental X-ray protein structures demonstrates that only 268 of the 1620 cysteine residues involve such phenylalanine-cysteine side chain interactions. Most of these interactions occur in the form of π (aromatic)-lone pair(sulphur) attractions, and correspond to a bonding energy less than 1.5 kcal mol^?1. A few were identified as the aromatic-thiol hydrogen bond with a bonding energy of 2.0–3.6 kcal mol^?1.     

Long-time behaviour of arbitrary order continuous time Galerkin schemes for some one-dimensional phase transition problems

The long-time behaviour of continuous time Galerkin (CTG) approximationsof some well-known one-dimensional non-linear evolution problemswhich model phase transitions are analyzed. These numericalschemes are fully discrete and of arbitrary order. Partially supported by the Army Research Office through grant28535-MA. Partially supported by the ONR Contract No N00014-90-J-1238.     

Acoustic Wave Propagation in an Underwater Sound Channel 1. Qualitative Theory

We give a qualitative study of wave propagation in an inhomogeneousmedium principally by geometrical optics and ray theory. Theinhomogeneity is represented by a sound-speed profile whichis dependent upon one coordinate, namely the depth; and we discussthe general characteristics of wave propagation which resultfrom a source placed on the sound channel axis. We show thatour mathematical model of the sound-speed in the ocean actuallypredicts some of the behaviour of the observed physical phenomenain the underwater sound channel. Using ray theoretic techniqueswe investigate the implications of our profile on the followingcharacteristics of SOFAR propagation: (i) the sound energy travellingfurther away from the axis takes less time to travel from sourceto receiver than sound energy travelling closer to the axis,(ii) the focusing of sound energy in the sound channel at certainranges, (iii) the overall ray picture in the sound channel.     

Numerical Studies of the Cahn-Hilliard Equation for Phase Separation

Phase separation in a binary mixture is described by the nonlinearevolutionary Cahn-Hilliard equation. In this paper, we discussthe physical background of the equation and describe its solutionby the Galerkin finite element method. Some theoretical resultsare presented and computationally verified.