Large scale molecular

S. K. Gray, D. W. Noid and B. G. Sumpter, Symplectic integrators for large scale molecular dynamics simulations A comparison of several explicit methods , J. Chem. Phys., Vol 101, no 5, 4062-72, 1994. 

Yamaguchi, Y. and Gspann, J., Large-Scale Molecular Dynamics Simulations of Cluster Impact and Erosion Processes on a Diamond Surface," Phys. Rev. B, Vol. 66, 2002, pp. 155408-1-10. 

The general approach is illustrated in detail for the case of aqueous ferrous and ferric ions, and the calculated rate constant and activation parameters are found to be in good agreement with the available experimental data. The formalisms we have employed in studying such complicated condensed phase processes necessarily rely on numerous approximations. Furthermore, some empirical data have been used in characterizing the solvated ions. We emphasize, nevertheless, that (1) none of the parameters were obtained from kinetic data, and (2) this is, as far as we are aware, the first such theoretical determination to be based on fully Ab initio electronic matrix elements, obtained from large scale molecular orbital (MO) calculations. A molecular orbital study of the analogous hexaaquo chromium system has been carried out by Hush, but the calculations were of an approximate, semi-empirical nature, based in part on experi-... 

Selective Quenching of Large-Scale Molecular Motions by Cross-Linking in the Strained State... 

The large scale molecular motions which take place in the rubber plateau and terminal zones of an uncross-linked linear polymer give rise to stress relaxation and thereby energy dissipation. For narrow molecular weight distribution elastomers non-catastrophic rupture of the material is caused by the disentanglement processes which occur in the terminal zone, e.g., by the reptation process. In practical terms it means that the green strength of the elastomer is poor. 

Because of the rarity of COS, there have been no large-scale molecular genetic studies of COS. However, at least two collaborative studies are planned for the coming years. 

This treatment assumes that the forces between molecules in relative motion are related directly to the thermodynamic properties of the solution. The excluded volume does indeed exert an indirect effect on transport properties in dilute solutions through its influence on chain dimensions. Also, there is probably a close relationship between such thermodynamic properties as isothermal compressibility and the free volume parameters which control segmental friction. However, there is no evidence to support a direct connection between solution thermodynamics and the frictional forces associated with large scale molecular structure at any level of polymer concentration. 

Further examination of the Williams approach seems called for, both to improve the method for estimating parameters such as the relaxation time, and to clarify the relationship between the intramolecular potential form and non-thermodynamic frictional forces. The method might provide a fairly unified description of non-linear flow porperties if a suitable potential function for large scale molecular friction were found. Aside from the Williams work, there have been no theoretical studies dealing with t] vs. y at low to moderate concentrations. The systematic changes in the master curve /(/ ) with coil overlap c[ij] are thus without explanation at the present time. 

In liquid crystals or LC-glasses one looks for orientational order and an absence of three-dimensional, long-range, positional order. In liquid crystals, large scale molecular motion is possible. In LC-glasses the molecules are fixed in position. The orientational order can be molecular or supermolecular. If the order rests with a supermolecular structure, as in soap micelles and certain microphase separated block copolymers, the molecular motion and geometry have only an indirect influence on the overall structure of the material. 

At the glass-transition temperature, the specific heat increases abruptly because the previously frozen large-scale molecular motions are now available to the chains for the uptake of thermal energy. The subsequent sharp downturn is due to crystallization... 

Kramers idea was to give a more realistic description of the dynamics in the reaction coordinate by including dynamical effects of the solvent. Instead of giving a deterministic description, which is only possible in a large-scale molecular dynamics simulation, he proposed to give a stochastic description of the motion similar to that of the Brownian motion of a heavy particle in a solvent. From the normal coordinate analysis of the activated complex, a reduced mass pi has been associated with the motion in the reaction coordinate, so the proposal is to describe the motion in that coordinate as that of a Brownian particle of mass g in the solvent. 

More realistic models were subsequently developed to incorporate many-body effects and realistic reaction mechanisms. Implementation of these in reduced dimensionality, small-scale simulations demonstrated the importance of the inclusion of these effects [161,162] however, the complexity of the functions and accompanying computational requirements prevent their use in large-scale molecular dynamics simulations in the condensed phase. 

At variance from Xe, the presented properties for Kr require more computional efforts. In order to reach the small-4 range of S(q), large-scale molecular dynamics have been carried out in the microcanonical ensemble (NVE) with the usual periodic boundary conditions. The equations of motion are integrated in the same discrete form as for Xe. The time step At is the same as for Xe and g r) is extracted over a sample of 8000 time-independent configurations every lOAf. 

Werner Cans, Alexander Blumen, and Anton Amann, Large-Scale Molecular Systems Quantum and Stochastic Aspects—Beyond the Simple Molecular Picture. Proceedings of the NATO Advanced Research Workshop held March 25-April 7, 1990, in Acquafredda di Maratea, Italy, in NATO ASI Series, Series B Physics, Vol. 258, Plenum, New York, 1991. 

Mike Gillan, Large Scale Molecular Simulation, in Mol. Simul., 14 (4-5), Gordon 8c Breach, Lausanne, 1995. 

The possible accumulation of negative ions at the air/ water interface was first predicted by Perera and Berkow-itz,8 who found out from molecular dynamics simulations, surprisingly, that the large anions (Cl , Br , and I ) are expelled from water clusters to their interface. Their predictions are supported by the recent large-scale molecular dynamics simulations for the air/water interface of various electrolyte solutions, which reveal that, when the polarization of ions and water molecules is explicitly taken into account, the large anions are accumulated near the interface.9... 

---