Cell dynamics simulations

Water molecules (density 1 g cm ) were placed uniformly within the periodic cell. Dynamics simulations were carried out at 298 K for 100 ps. Time steps were set at 0.001 ps and a Berendsen thermostat was used with a time step of 0.5 ps. Typically, 20 ps were used for equilibration runs, followed by production runs of 80 ps. 

The kinetics of ordering in block copolymer melts have been studied using cell dynamics simulations of the TDGL equation (Bahiana and Oono 1990 Chakrabarti et al. 1991 Puri and Oono 1988 Qi and Wang 1996, 1997 Shiwa et al. 1996). Here, the time evolution of the order parameter ip is followed ... 

The evolution of a system described by an equation related to eqn 2.26 was studied using cell dynamics simulations by Oono and co-workers (Bahiana and Oono 1990 Puri and Oono 1988). In the CDS method the continuous order parameter is discretized on a lattice and at time t is denoted where n labels... 

Fig. 2.46 Cell-dynamical simulation of a symmetric block copolymer in two dimensions (64 X 64 lattice) (Hamley 1997).This structure forms from an initially homogeneous state via time-dependent Ginzburg-Landau kinetics at a temperature below the ODT.

Boltzmann and cell dynamics simulations. Non-linear flows are experienced when processing block copolymer thermoplastic elastomers, and this subject is thus likely to attract industrial and academic interest. Molecular models will provide insight into the viscoelasticity at higher frequencies. 

Computer simulations in the mesoscopic regime are now possible using methods such as Lattice Bolztmann, Dissipative Particle Dynamics, MesoDyn and Cell Dynamics Simulations. MesoDyn is a commercial package (from... 

MSI) that uses the same time-dependent Ginzburg Landau kinetic equation as CDS, but starts from (arbitrary) bead models for polymer chains. The methods have been summarized elsewhere. Examples of recent applications include LB simulations of viscoelastic effects in complex fluids under oscillatory shear,DPD simulations of microphase separation in block copoly-mers ° and mesophase formation in amphiphiles, and cell dynamics simulations applied to block copolymers under shear. - DPD is able to reproduce many features of analytical mean field theory but in addition it is possible to study effects such as hydrodynamic interactions. The use of cell dynamics simulations to model non-linear rheology (especially the effect of large amplitude oscillatory shear) in block copolymer miscrostructures is currently being investigated. ... 

Pinna, M Zvelindovsky, A.V., Todd, S and Goldbeck-Wood, G. (2006) Cubic phases of block copolymers under shear and electric fields by cell dynamics simulation. /. Chem. Pkys., 125 (15), 154905. 

Cell dynamics simulations are based on the time dependence of an order parameter, (i) (Eq. 1.23), which varies continuously with coordinate r. For example, this can be the concentration of one species in a binary blend. An equation is written for the time evolution of the order parameter, dir/dt, in terms of the gradient of a free energy that controls, for example, the tendency for local diffusional motions. The corresponding differential equation is solved on a lattice, i.e. the order parameter V (r) is discretized on a lattice, taking a value at lattice point i. This method is useful for modelling long time-scale dynamics such as those associated with phase separation processes. 

The melt-phase behaviour of block copolymers has been theoretically examined by many researchers using the self-consistent mean-field theory (SCFT), cell dynamics simulations, and so forth. Especially, it is noteworthy that Matsen and Bates [10] have constructed the phase diagram for an A-B diblock... 

Dynamic Simulation of Plate-Type Reformer and Combustor System for Molten Carbonate Fuel Cell... 

Similar schemes to the above can be used in molecular dynamics simulations in other ensembles such as those at constant temperature or constant pressure (see Frenkel and Smit, and Allen and Tildesley (Further reading)). A molecular dynamics simulation is computationally much more intensive than an energy minimization. Typically with modern computers the real time sampled in a simulation run for large cells is of the order of nanoseconds (106 time steps). Dynamical processes operating on longer time-scales will thus not be revealed. 

The second approach used in first-principles tribological simulations focuses on the behavior of the sheared fluid. That is, the walls are not considered and the system is treated as bulk fluid, as discussed. These simulations are typically performed using ab initio molecular dynamics (AIMD) with DFT and plane-wave basis sets. A general tribological AIMD simulation would be run as follows. A system representing the fluid would be placed in a simulation cell repeated periodically in all three directions. Shear or load is applied to the system using schemes such as that of Parrinello and Rahman, which was discussed above. In this approach, one defines a (potentially time-dependent) reference stress tensor aref and alters the nuclear and cell dynamics, such that the internal stress tensor crsys is equal to aref. When crsys = aref, the internal and external forces on the cell vectors balance, and the system is subject to the desired shear or load. 

When performing variable-cell AIMD simulations with plane-wave basis sets, problems originate from the fact that the basis set is not complete with respect to the cell vectors.71 This incompleteness can introduce fictitious forces (Pulay forces) into asys and lead to artificial dynamics. To overcome this problem, one must ensure that asys is well converged with respect to the basis set size. In general, it is found that one needs to employ a plane-wave kinetic... 

Y. Nakayama, A. Kinoshita, and M. Tomita, Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor. Biol. Med. Model. 2(1), 18... 

Encouraging progress has been made recently, and we are now in an era of active application of molecular dynamics simulation to study the folding process. Because of the vital importance of water in protein folding and in the cell, the explicit repre-... 

Fig. 26 Molecular dynamics simulation cell of (S)-phenylalanine intercalated in an Mg/Al LDH. Reprinted with permission from [225]. Copyright American Chemical Society...

Andre, S. Pei, Z. Siebert, H.-C. Ramstrom, O. Cabins, H.-J. Glycosyl-disulfides from dynamic combinatorial libraries as O-glycoside mimetics for plant and endogenous lectins Their reactivities in solid-phase and cell assays and conformational analysis by molecular dynamics simulations. Bioorg. Med. Chem. 2006,14, 6314-6326. 

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