Simulation of Structures

PLATE XIII Molecular graphics representation of structure of simulated Ti-wadeite glass. The colours for atoms are the same as those in Plate XII. 

PLATE XIV Structure of simulated A1P04 at a pressure of (a) OGPa, (b) 13GPa, (c) 29GPa, and (d) 33GPa. Yellow spheres are aluminium atoms, purple spheres are phosphorus atoms and blue spheres are oxygen atoms. 

Dickinson, E. and S.R. Euston. 1992. Short-range structure of simulated floes of particles with bridging polymer. Colloids and Surfaces 62 (3) 231-242. 

In addition, on the basis of analogous specimens, the accumulation of damage and plastic deformation of metal structure were simulated. These results provide the possibility to obtain the prediction charts of the metal work s residual resource. 

Neumann M and Steinhauser O 1980 The influence of boundary conditions used in machine simulations on the structure of polar systems Mol. Phys. 39 437-54... 

A multitude of different variants of this model has been investigated using Monte Carlo simulations (see, for example [M])- The studies aim at correlating the phase behaviour with the molecular architecture and revealing the local structure of the aggregates. This type of model has also proven useful for studying rather complex structures (e.g., vesicles or pores in bilayers). 

Lattice models have been studied in mean field approximation, by transfer matrix methods and Monte Carlo simulations. Much interest has focused on the occurrence of a microemulsion. Its location in the phase diagram between the oil-rich and the water-rich phases, its structure and its wetting properties have been explored [76]. Lattice models reproduce the reduction of the surface tension upon adsorption of the amphiphiles and the progression of phase equilibria upon increasmg the amphiphile concentration. Spatially periodic (lamellar) phases are also describable by lattice models. Flowever, the structure of the lattice can interfere with the properties of the periodic structures. 

Another set of simulations was carried out with the targeted molecular dynamics (TMD) method (Schlitter et ah, 1993). The initial and final structures of an SMD simulation were used as input for the TMD simulations as discussed in Methods . TMD trajectories were calculated in both directions between the input structures, simulating both the binding and the... 

The SMD simulations were based on an NMR structure of the Ig domain 127 of the cardiac titin I-band (Improta et ah, 1996). The Ig domains consist of two /9-sheets packed against each other, with each sheet containing four strands, as shown in Fig. 8b. After 127 was solvated and equilibrated, SMD simulations were carried out by fixing one terminus of the domain and applying a force to the other in the direction from the fixed terminus to the other terminus. Simulations were performed as described by Eq. (1) with V = 0.5 A/ps and if = 10 ksT/A 414 pN/A. The force-extension profile from the SMD trajectory showed a single force peak as presented in Fig. 8a. This feature agrees well with the sawtooth-shaped force profile exhibited in AFM experiments. 

M. H. Hao, M. R. Pincus, S. Rackovsky, and H. A. Scheraga. Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations. Biochemistry, 32 9614-9631, 1993. 

Abstract. The overall Hamiltonian structure of the Quantum-Classical Molecular Dynamics model makes - analogously to classical molecular dynamics - symplectic integration schemes the methods of choice for long-term simulations. This has already been demonstrated by the symplectic PICKABACK method [19]. However, this method requires a relatively small step-size due to the high-frequency quantum modes. Therefore, following related ideas from classical molecular dynamics, we investigate symplectic multiple-time-stepping methods and indicate various possibilities to overcome the step-size limitation of PICKABACK. 

Abstract. This paper presents results from quantum molecular dynamics Simula tions applied to catalytic reactions, focusing on ethylene polymerization by metallocene catalysts. The entire reaction path could be monitored, showing the full molecular dynamics of the reaction. Detailed information on, e.g., the importance of the so-called agostic interaction could be obtained. Also presented are results of static simulations of the Car-Parrinello type, applied to orthorhombic crystalline polyethylene. These simulations for the first time led to a first principles value for the ultimate Young s modulus of a synthetic polymer with demonstrated basis set convergence, taking into account the full three-dimensional structure of the crystal. 

The structure of the metallocene cation energy minimised with the Car-Parrinello method agrees well with the experimentally obtained crystal structures of related complexes. Typical features of the structure as obtained from X-ray diffraction on crystals of very similar neutral complexes (e.g., the dichlorides), such as small differences in distances between C atoms within a cyclopentadienyl (Cp) ring, as well as differences in distances between the C atoms of the Cp ring and the Zr atom, were revealed from the simulations. 

Many problems in force field investigations arise from the calculation of Coulomb interactions with fixed charges, thereby neglecting possible mutual polarization. With that obvious drawback in mind, Ulrich Sternberg developed the COSMOS (Computer Simulation of Molecular Structures) force field [30], which extends a classical molecular mechanics force field by serai-empirical charge calculation based on bond polarization theory [31, 32]. This approach has the advantage that the atomic charges depend on the three-dimensional structure of the molecule. Parts of the functional form of COSMOS were taken from the PIMM force field of Lindner et al., which combines self-consistent field theory for r-orbitals ( nr-SCF) with molecular mechanics [33, 34]. 

Figure 7-15 shows the time evolution of the temperature, total energy, and potential energy for a 300 ps simulation of the tetracycline repressor dimer in its induced (i.e., hgand-bound) form. Starting from the X-ray structure of the monomer in a complex with one molecule of tetracycline and a magnesium ion (protein database... 

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

Infrared spectra are strongly dependent on the 3D structure of a compound, as reflected by the success of attempts to simulate infrared spectra from 3D structure representations (see Section 10.2.5). Infrared spectra should therefore be taken as representations of a chemical compound for modeling properties that are suspected to be dependent on the 3D structure of a compound NMR spectra also depend on... 

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