Computational aspects

S. Gupta, Computing aspects of molecular dynamics simulation , Comp. Phys. Comm., Vol 70, no 2, 243-70, 1992. 

Casey, J. and Naghdi, P.M., Constitutive Results for Finitely Deforming Elastic-Plastic Materials, in Constitutive Equations Macro and Computational Aspects (edited by K.J. Wiliam), ASME, 1984, pp. 53-71. 

Besides the above-mentioned problems with step control, there are also other computational aspects which tend to make the straightforward NR problematic for many problem types. The true NR method requires calculation of the full second derivative matrix, which must be stored and inverted (diagonalized). For some function types a calculation of the Hessian is computationally demanding. For other cases, the number of variables is so large that manipulating a matrix the size of the number of variables squared is impossible. Let us address some solutions to these problems. 

Clementi, Enrico, Computational Aspects for Large Chemical Systems. Berlin Springer-Verlag, 1980. 

Gaussian-type orbitals, the computational requirements grow, in the limit, with the fourth power in the number of basis functions on the SCF level and with even a higher power for methods including correlation. Both the conceptual and the computational aspects prevent the computational study of important problems such as the chemistry of transition metal surfaces, interfaces, bulk compounds, and large molecular systems. 

TOO Schwerdtfeger, P. (2006) Atomic Static Dipole Polarizabilities, in Computational Aspects of Electric Polarizability Calculations Atoms, Molecules and Clusters (ed. G. Maroulis), Imperial College Press, London, pp. 1-32. 

S. Van Huffel and J. Vandewalle, The Total Least Squares Problem Computational Aspects and Analysis. SIAM, Philadelphia, PA, 1991. 

Implementation tools differ in the facilities they offer. A major selection criterion is the knowledge representation possibilities the tools offer. Another important issue is the access to external programs. This is an important aspect for chemical knowledge bases since many chemical problems involve a large computational aspect that is best solved by an external, algorithmic program. 

The scope of this review is to summarize the recent development of the solution NMR to DD from aqueous phase to lipid bilayer membranes on the basis of our recent NMR work. Relevant physicochemical and computational aspects of the membrane DD are also referred to here. 

Rice BM, Byrd EFC, Mattson WD (2007) Computational Aspects of Nitrogen-Rich HEDMs. 125 153-194... 

The approximate transferability of fuzzy fragment density matrices, and the associated technical, computational aspects of the idempotency constraints of assembled density matrices, as well as the conditions for adjustability and additivity of fragment density matrices are discussed in Section 4, whereas in Section 5, an algorithm for small deformations of electron densities are reviewed. The Summary in Section 6 is followed by an extensive list of relevant references. 

When the simulation of deep-well temperatures, pressures, and salinities is imposed as a condition, the number of codes that may be of value is reduced to a much smaller number. Nordstrom and Ball121 recommend six references as covering virtually all the mathematical, thermodynamic, and computational aspects of chemical-equilibrium formulations (see references 123-128). Recent references on modeling include references 45, 63, 70, 129, and 130. 

Theory and computational aspects of intestinal permeability have been reviewed in detail by Egan and Lauri [27], Briefly, a drug must be somewhat permeable through the membrane of the intestinal tract if it is to be administered orally and achieve systemic exposure. The rate of membrane permeability is strongly related to the lipophilicity and hydrophilicity of the molecule. Thus, models with a small number of descriptors related to those two properties can provide useful predictions of drug absorption. 

The focus of the next four chapters (Chapters 14-17) is mainly on the theoretical/computational aspects. Chapter 14 by T. S. Sorensen and E. C. F. Yang examines the involvement of p-hydrido cation intermediates in the context of the industrially important heptane to toluene dehydrocyclization process. Chapter 15 by P. M. Esteves et al. is devoted to theoretical studies of carbonium ions. Chapter 16 by G. L. Borosky and K. K. Laali presents a computational study on aza-PAH carbocations as models for the oxidized metabolites of Aza-PAHs. Chapter 17 by S. C. Ammal and H. Yamataka examines the borderline Beckmann rearrangement-fragmentation mechanism and explores the influence of carbocation stability on the reaction mechanism. 

Hall LH (1990) In Rouvray DH (ed) Computational aspects of molecular connectivity and its role in structure-property modeling computational chemical graph theory. Nova Science Publishers, New York, NY, chap 8, p 202... 

The article is organized as follows. The main features of the linear response theory methods at different levels of correlation are presented in Section 2. Section 3 describes the calculation of the dipole and quadmpole polarizabilities of two small diatomic molecules LiH and HF. Different computational aspects are discussed for each of them. The LiH molecule permits very accurate MCSCF studies employing large basis sets and CASs. This gives us the opportunity to benchmark the results from the other linear response methods with respect to both the shape of the polarizability radial functions and their values in the vibrational ground states. The second molecule, HF, is undoubtedly one of the most studied molecules. We use it here in order to examine the dependence of the dipole and quadmpole polarizabilities on the size of the active space in the CAS and RASSCF approaches. The conclusions of this study will be important for our future studies of dipole and quadmpole polarizabilities of heavier diatomic molecules. 

Martin, Y.C. Diverse viewpoints on computational aspects of molecular diversity./. Comb. Chem. 2001, 3, 231-250. 

Martin, Y.C. Diverse viewpoints on computational aspects of molecular... 

The Patai Series publishes comprehensive reviews on all aspects of specific functional groups. Each volume contains outstanding surveys on theoretical and computational aspects, NMR, MS, other spectroscopical methods and analytical chemistry, structural aspects, thermochemistry, photochemistry, synthetic approaches and strategies, synthetic uses and applications in chemical and pharmaceutical industries, biological, biochemical and environmental aspects. 

Considering such recent relevance of SDP in quantum chemistry, this chapter discusses some practical aspects of this variational calculation of the 2-RDM formulated as an SDP problem. We first present the definition of an SDP problem, and then the primal and dual SDP formulations of the variational calculation of the 2-RDM as SDP problems (Section II), an efficient algorithm to solve the SDP problems the primal-dual interior-point method (Section III), a brief section about alternative and also efficient augmented Lagrangian methods (Section IV), and some computational aspects when solving the SDP problems (Section V). 

The Human Genome Project went three-dimensional in late 2000. Structural genomics efforts will determine the structures of thousands of new proteins over the next decade. These initiatives seek to streamline and automate every experimental and computational aspect of the structural determination pipeline, with most of the steps involved covered in previous chapters of this volume. At the end of the pipeline, an atomic model is built and iteratively refined to best fit the observed data. The final atomic model, after careful analysis, is deposited in the Protein Data Bank, or PDB (Berman et ah, 2000). About 25,000 unique protein sequences are currently in the PDB. High-throughput and conventional methods will dramatically increase this number and it is crucial that these new structures be of the highest quality (Chandonia and Brenner, 2006). 

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