Simulation computational methods

CCCII comprises ten volumes, of which the last contains only subject indexes. The first two volumes describe the development of new ligands since the 1980s, which complements Volume 2 in CCC. They also include new techniques of synthesis and characterization, with a special emphasis on the burgeoning physical techniques which are increasingly applied to the study of coordination compounds. Developments in theory, computation methods, simulation, and useful software are reported. The volumes conclude with a series of case studies, which illustrate how synthesis, spectroscopy, and other physical techniques have been successfully applied in unravelling some significant problems in coordination chemistry. 

Recently, molecular dynamics and Monte Carlo calculations with quantum mechanical energy computation methods have begun to appear in the literature. These are probably some of the most computationally intensive simulations being done in the world at this time. 

Ramirez, W. F. Computational Methods for Process Simulations. Butter-worths, Boston (1989). 

Computational methods have played an exceedingly important role in understanding the fundamental aspects of shock compression and in solving complex shock-wave problems. Major advances in the numerical algorithms used for solving dynamic problems, coupled with the tremendous increase in computational capabilities, have made many problems tractable that only a few years ago could not have been solved. It is now possible to perform two-dimensional molecular dynamics simulations with a high degree of accuracy, and three-dimensional problems can also be solved with moderate accuracy. 

In Section II we provide an overview of the current status of nucleic acid simulations, including studies on small oligonucleotides, DNA, RNA, and their complexes with proteins. This is followed a presentation of computational methods that are currently being applied for the study of nucleic acids. The final section of the chapter includes a number of practical considerations that may be useful in preparing, performing, and analyzing MD simulation based studies of nucleic acids. 

Very recently, people who engage in computer simulation of crystals that contain dislocations have begun attempts to bridge the continuum/atomistic divide, now that extremely powerful computers have become available. It is now possible to model a variety of aspects of dislocation mechanics in terms of the atomic structure of the lattice around dislocations, instead of simply treating them as lines with macroscopic properties (Schiotz et al. 1998, Gumbsch 1998). What this amounts to is linking computational methods across different length scales (Bulatov et al. 1996). We will return to this briefly in Chapter 12. 

The bond fluctuation model (BFM) [51] has proved to be a very efficient computational method for Monte Carlo simulations of linear polymers during the last decade. This is a coarse-grained model of polymer chains, in which an effective monomer consists of an elementary cube whose eight sites on a hypothetical cubic lattice are blocked for further occupation (see... 

In a similar way, computational chemistry simulates chemical structures and reactions numerically, based in full or in part on the fundamental laws of physics. It allows chemists to study chemical phenomena by running calculations on computers rather than by examining reactions and compounds experimentally. Some methods can be used to model not only stable molecules, but also short-lived, unstable intermediates and even transition states. In this way, they can provide information about molecules and reactions which is impossible to obtain through observation. Computational chemistry is therefore both an independent research area and a vital adjunct to experimental studies. 

Owing to the increasing efficiency of computational methods, it has become possible to investigate base pairs in the gas phase and solution simulated by super-molecular approaches with up to six water molecules [98IJQ37, 98JPC(A) 10374, 98JPC(B)9109, 99JST107]. In the cytosine-isocytosine Watson-Crick base pair. 

The purification of value-added pharmaceuticals in the past required multiple chromatographic steps for batch purification processes. The design and optimization of these processes were often cumbersome and the operations were fundamentally complex. Individual batch processes requires optimization between chromatographic efficiency and enantioselectivity, which results in major economic ramifications. An additional problem was the extremely short time for development of the purification process. Commercial constraints demand that the time interval between non-optimized laboratory bench purification and the first process-scale production for clinical trials are kept to a minimum. Therefore, rapid process design and optimization methods based on computer aided simulation of an SMB process will assist at this stage. 

Since the middle of the 1990s, another computation method, direct simulation Monte Carlo (DSMC), has been employed in analysis of ultra-thin film gas lubrication problems [13-15]. DSMC is a particle-based simulation scheme suitable to treat rarefied gas flow problems. It was introduced by Bird [16] in the 1970s. It has been proven that a DSMC solution is an equivalent solution of the Boltzmann equation, and the method has been effectively used to solve gas flow problems in aerospace engineering. However, a disadvantageous feature of DSMC is heavy time consumption in computing, compared with the approach by solving the slip-flow or F-K models. This limits its application to two- or three-dimensional gas flow problems in microscale. In the... 

Refinement of Conformations by Computational Methods 243 9.4.2.6 Simulated Annealing (SA)... 

RS Thomas, WE Lytle, TJ Keefe, AA Constan, RSH Yang. Incorporating Monte Carlo simulation into physiologically based pharmacokinetic models using advanced continuous simulation language (ACSL) A computational method. Fundam Appl Toxicol 31 19-28, 1996. 

In this review the status of the relevant technology will be assessed with particular reference to formulation of problems and methods of solution. We shall, for the most part, be concerned with the technical literature of the last ten years. Since that period corresponds to the total eclipse of analog simulation which had been previously used, to some extent, in modeling pipeline networks (R3), we shall focus exclusively on digital computation methods. However, we shall not be content with a mere catalog of the different... 

Straub, J.E. Andricioaei, I., Computational methods inspired by Tsallis statistics Monte Carlo and molecular dynamics algorithms for the simulation of classical and quantum systems, Braz. J. Phys. 1999, 29, 179-186... 

Andricioaei, I. Straub, J.E., Computational methods for the simulation of classical and quantum many body systems sprung from the nonextensive thermostatistics. In Nonextensive Statistical Mechanics and Its Application, Abe, S. Okamoto, Y., Eds., Lecture Notes in Physics. Springer Berlin, Heidelberg, New York, 2001, ch. IV, pp. 195-235... 

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