Molecular dynamics analysis

J. Gao, K. Kuczera, B. Tldor, and M. Karplus. Hidden thermodynamics of mutant proteins A molecular dynamics analysis. Science, 244 1069-1072, 1989. 

Fiber, R. Karplus, M. Multiple conformational states of proteins a molecular dynamics analysis of myoglobin. Science 235 318-321, 1987. 

It has been proposed that the metal ion also has an interaction with the pro-Rp oxygen atom at the scissile phosphate, Pi.i. However, the scissile phosphodiester bond, within the crystal structure, is located approximately 20 A from the A9/G10.1 site [96]. It should be true that a conformationd change occurs to rotate the initial structure that is not feasible for the inhne attack to in-line structure around the scissile phosphate, but molecular dynamics analysis denies to arrange A9/G10.1 to come close to Pi.i via a metal ion. Furthermore, although it has been suggested that there is a weak interaction of a metal ion with the oxygen atom at P 1.1, our recent experiments observed no interaction of a metal ion with the Pi.i phosphate by kinetic and NMR analyses [97, 98]. 

C. M. Morales and W. H. Thompson. Mixed quantum-classical molecular dynamics analysis of the molecular-level mechanisms of vibrational frequency shifts. J.Phys. Chem. A, lll(25) 5422-5433, JUN 28 2007. 

Zuniga, I. Bahar, R. Dodge, and W. L. Mattice,/. Chem. Phys., 95, 5348 (1991). Molecular Dynamics Analysis of Transitions between Rotational Isomers in Polymethylene. 

Zhao X, Huang X, Sun C. Molecular dynamics analysis of the engrailed homeodomain-DNA recognition. J. Struct. Biol. 2006 155 426-437. 

R. Elber and M. Karpins (1987) Multiple conformational states of proteins A molecular dynamics analysis of Myoglobin. Science 235, pp. 318-321 P. Deuflhard, W. Huisinga, A. Fischer, and C. Schiitte (2000) Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains. Lin. Alg. Appl. 315, pp. 39-59... 

Gao, J., Kuczera, K., Tidor, B., Karplus, M. Hidden thermodynamics of mutant proteins—a molecular-dynamics analysis. Science 1989, 244,1069-72. 

Palmer, A.G., Case, D.A. Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide. J. Am. Chem. Soc. 1992,114,9059-67. 

DS has been demonstrated to be a useful tool for the analysis of the glass transition phenomenon in both natural and synthetic polymers, especially under the influence of water, and its application on composites molecular dynamics analysis was also demonstrated [5-7]. This chapter addresses the glass transition phenomenon from an experimental standpoint by exploring a dielectric method used for the characterization of the glass transition phenomenon in natural and synthetic polymers. 

In polymers, the glass transition phenomenon has been related to the dielectric a-relaxation processes through the Vogel-Fulcher-Tammann (VET) equation [9], and it can be characterized by means of their molecular dynamics analysis. 

R. Elber and M. Karplus, Science, 235, 318 (1987). Multiple Conformational States of Proteins A Molecular Dynamics Analysis of Myoglobin. 

Sieker, R, Springer, S., and Zacharias, M. Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles. Protein Sci, 16(2) 299-308 (2007). 

Dianoux, A.J., G.R Kneller, J.L. Sauvajol, and J.C. Smith. 1993. The polarized density-of-states of crystalline polyacetylene-molecular-dynamics analysis and comparison with neutron-scattering results. 7 Chem Phys 99 5586. 

Zacate, M. O., Minervini, L., Bradfield, D. J., Grimes, R. W., and Sickafus, K. E. (2000). Defect cluster formation in M2O3-doped cubic Zr02- Solid State Ionics 128 243-254. Yamamuru, Y., Kawasaki, S., and Sakai, H. (1999). Molecular dynamics analysis of ionic conduction mechanism in yttria-stabilized zirconia. Solid State Ionics 126 181-189. 

Method Based on the Meshfree Method and Molecular Dynamics Analysis. 

Thus, the observed decrease in the intensity of bands of low-frequency skeletal vibrations indicates that the vibrational motion considered is gradually suppressed as the cross-link spacing approaches the length of the correlation chain part. This result agrees well with the molecular dynamics analysis of a polymer chain with a rigid cross-link [116]. Presumably, these diain vilHations are related to equilibrium chain ri dity, and the chain part involved in this motion is commensurate with the Kuhn segment. 

Molecular dynamics analysis of point defects in silicon near solid-liquid interface , Appl. Surface Sd. 159-160, 378-391. 

Yamamuru, Y., Kawasaki, S. and H. Sakai (1999), Molecular dynamics analysis of ionic conduction mechanism in yttria-stabilized zirconia, Solid State Ionics, 126, 181-89. 

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