Overview of Computational Research

Experimental research has shown that a vapor cloud explosion can be described as a process of combustion-driven expansion flow with the turbulent structure of the flow acting as a positive feedback mechanism. Combustion, turbulence, and gas dynamics in this complicated process are closely interrelated. Computational research has explored the theoretical relations among burning speed, flame speed, combustion rates, geometry, and gas dynamics in gas explosions. 

The combustion-flow interactions should be central in the computation of combustion-generated flow fields. This interaction is fundamentally multidimensional, and can only be computed by the most sophisticated numerical methods. A simpler approach is only possible if the concept of a gas explosion is drastically simplified. The consequence is that the fundamental mechanism of blast generation, the combustion-flow interaction, cannot be modeled with the simplified approach. In this case flame propagation must be formalized as a heat-addition zone that propagates at some prescribed speed. 

Analytical methods relate the gas dynamics of the expansion flow field to an energy addition that is fully prescribed. A first step in this approach is to examine spherical geometry as the simplest in which a gas explosion manifests itself. The gas dynamics of a spherical flow field is described by the conservation equations for mass, momentum, and energy  

This section describes how this set of equations can be solved analytically by the introduction of various simplifications. First, gas dynamics is linearized, thus permitting an acoustic approach. Next, a class of solutions based on the similarity principle is presented. The simplest and most tractable results are obtained from the most extensive simplifications. 

The solution of the wave equation must be an expression of the form ) = (1/r) 

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The modeling of carbohydrates is undergoing rapid development. For example, the first comprehensive conformational mappings of disaccharides with flexible residues and the first molecular dynamics studies of carbohydrates have only recently been published. At the same time, interest in carbohydrates has been increasing dramatically, and there is a need for a publication that gently introduces the uninitiated and provides an overview of current research in the area. We feel that Computer Modeling ( Carbohydrate Molecules meets these needs. 

This conversational and somewhat subjective overview of computational approaches in zeolite chemistry has illustrated that the field is very diverse, and expanding rapidly. Modeling and simulation at the atomistic or electronic structural level clearly contribute at various levels to practical zeolite research and development programs. Characterization and zeolite physical and chemical property prediction are the most prominent application domains at present. 

In Chapter 5 the Penn State group of K. V. Damodaran and Kenneth M. Merz Jr. review lipid systems. Merz s research in computational chemistry spans the range from applied bonding theory of small organic molecules to simulations of biophysical processes. Membranes are an important component of living systems and are now the focus of much research. An overview of computer simulation of lipid systems is warranted. It is to be noted that this is the first chapter in Review in Computational Chemistry that discusses a class of molecules rather than a technique of computation. As time progresses we will... 

Varma, V.A., Reklaitis, G.V., Blau, G.E., and Pekny J.F. (2007) Enterprise-wide modeling and optimization - an overview of emerging research challenges and opportunities. Computers el Chemical Engineering, 31 (5-6), 692-711. 

In combination, the book should serve as a useful reference for both theoreticians and experimentalists in all areas of biophysical and biochemical research. Its content represents progress made over the last decade in the area of computational biochemistry and biophysics. Books by Brooks et al. [24] and McCammon and Harvey [25] are recommended for an overview of earlier developments in the field. Although efforts have been made to include the most recent advances in the field along with the underlying fundamental concepts, it is to be expected that further advances will be made even as this book is being published. To help the reader keep abreast of these advances, we present a list of useful WWW sites in the Appendix. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Abstract A review is provided on the contribution of modern surface-science studies to the understanding of the kinetics of DeNOx catalytic processes. A brief overview of the knowledge available on the adsorption of the nitrogen oxide reactants, with specific emphasis on NO, is provided first. A presentation of the measurements of NO, reduction kinetics carried out on well-characterized model system and on their implications on practical catalytic processes follows. Focus is placed on isothermal measurements using either molecular beams or atmospheric pressure environments. That discussion is then complemented with a review of the published research on the identification of the key reaction intermediates and on the determination of the nature of the active sites under realistic conditions. The link between surface-science studies and molecular computational modeling such as DFT calculations, and, more generally, the relevance of the studies performed under ultra-high vacuum to more realistic conditions, is also discussed. 

The explosive growth in the availability of computer tools In the laboratory requires a new look at the concept of laboratory automation. Much larger gains in the efficiency and effectiveness of research can be realized by automating tasks rather than by simply automating instruments. Research is done by researchers, not by instruments. Instruments are Just one of many tools which can be used by the researcher. This paper will attempt to give an overview of instrument automation as the traditional view of laboratory automation, and extend this concept to the automation of the total task of research. 

The volume is organized in thirteen chapters. The first of them makes a brief overview of the computational methods available for this field of chemistry, and each of the other twelve chapters reviews the application of computational modeling to a particular catalytic process. Their authors are leading researchers in the field, and because of this, they give the reader a first hand knowledge on the state of the art. 

Appendix B consists of a systematic classification and review of conceptual models (physical models) in the context of PBC technology and the three-step model. The overall aim is to present a systematic overview of the complex and the interdisciplinary physical models in the field of PBC. A second objective is to point out the practicability of developing an all-round bed model or CFSD (computational fluid-solid dynamics) code that can simulate thermochemical conversion process of an arbitrary conversion system. The idea of a CFSD code is analogue to the user-friendly CFD (computational fluid dynamics) codes on the market, which are very all-round and successful in simulating different kinds of fluid mechanic processes. A third objective of this appendix is to present interesting research topics in the field of packed-bed combustion in general and thermochemical conversion of biofuels in particular. 

One of the main problems for the annotation and classification of the biological space is the lack of a standard scheme for all protein families. Even within families, different classification schemes coexist and are being used by different research communities. This aspect hampers enormously any chemogenomic initiative aimed at integrating chemical and biological spaces with novel computational techniques. The following provides an overview of the classification schemes currently in use for the main therapeutically relevant protein families. 

Brinkerhoff, J. D., J. D. Klein, and C. M. Koroghlanian (2001) Effects of overviews and computer experience on learning from hypertext. Journal of Educational Computing Research 25(4), 427 140. 

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