Difference explicit

Relaxation via processes (iii), (iv), and (v) is treated in a somewhat similar way to that of dipolar relaxation, the source of the coupling to the surroundings being different. Explicit expressions for the relaxation times in terms of the constants of the interactions have been derived. 

Task decomposition. In the PCA the task decomposition is unique, i.e., there are no different explicit tasks to evaluate in order to select the best one. In the case of normal operation of the plant this is perfectly right but the RCS allows in the presence of faults (detected by the SPs and WM) to select new different tasks. 

In short, it would be more sensible to be able to use different explicit models for different electronic sub-structures of a molecule. 

Two different explicit schemes have been shown to be particularly efficient in order to propagate the wavepacket in time ... 

It is very important, from one hand, to accept a hypothesis about the material fracture properties before physical model building because general view of TF is going to change depending on mechanical model (brittle, elasto-plastic, visco-elasto-plastic, ete.) of the material. From the other hand, it is necessary to keep in mind that the material response to loads or actions is different depending on the accepted mechanical model because rheological properties of the material determine type of response in time. The most remarkable difference can be observed between brittle materials and materials with explicit plastic properties. 

Problems arise if a light pulse of finite duration is used. Here, different frequencies of the wave packet are excited at different times as the laser pulse passes, and thus begin to move on the upper surface at different times, with resulting interference. In such situations, for example, simulations of femtochemistry experiments, a realistic simulation must include the light field explicitely [1]. 

Figure 9. Energy difference (absolute value) between the components of the X II electronic State of HCCS as a function of coordinates p, P2, and y. Curves represent the square root of the second of functions given by Eq. (77) (with e, = —0.011, 2 = 0.013, 8,2 = 0.005325) for fixed values of coordinates p, and P2 (attached at each curve) and variable Y = 4>2 Here y = 0 corresponds to cis-planar geometry and y = 71 to trans-planar geometry. Symbols results of explicit ab initio calculations.

The interaction with the solvent is of similar importance as the intramolecuiar energy contributions and a correct representation of the solvent is therefore es.sential. If an explicit solvent description is chosen, averaging over many different solvent configurations is necessary in order to obtain converged statistical averages. Advantageous in this respect is describing the solvent as... 

A reasonable approach for achieving long timesteps is to use implicit schemes [38]. These methods are designed specifically for problems with disparate timescales where explicit methods do not usually perform well, such as chemical reactions [39]. The integration formulas of implicit methods are designed to increase the range of stability for the difference equation. The experience with implicit methods in the context of biomolecular dynamics has not been extensive and rather disappointing (e.g., [40, 41]), for reasons discussed below. 

Another view of this theme was our analysis of spectral densities. A comparison of LN spectral densities, as computed for BPTI and lysozyme from cosine Fourier transforms of the velocity autocorrelation functions, revealed excellent agreement between LN and the explicit Langevin trajectories (see Fig, 5 in [88]). Here we only compare the spectral densities for different 7 Fig. 8 shows that the Langevin patterns become closer to the Verlet densities (7 = 0) as 7 in the Langevin integrator (be it BBK or LN) is decreased. 

Another difference is related to the mathematical formulation. Equation (1) is deterministic and does not include explicit stochasticity. In contrast, the equations of motion for a Brownian particle include noise. Nevertheless, similar algorithms are adopted to solve the two differential equations as outlined below. The most common approach is to numerically integrate the above differential equations using small time steps and preset initial values. 

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

It is often the case that the solvent acts as a bulk medium, which affects the solute mainly by its dielectric properties. Therefore, as in the case of electrostatic shielding presented above, explicitly defined solvent molecules do not have to be present. In fact, the bulk can be considered as perturbing the molecule in the gas phase , leading to so-called continuum solvent models [14, 15]. To represent the electrostatic contribution to the free energy of solvation, the generalized Bom (GB) method is widely used. Wilhin the GB equation, AG equals the difference between and the vacuum Coulomb energy (Eq. (38)) ... 

The problem with most quantum mechanical methods is that they scale badly. This means that, for instance, a calculation for twice as large a molecule does not require twice as much computer time and resources (this would be linear scaling), but rather 2" times as much, where n varies between about 3 for DFT calculations to 4 for Hartree-Fock and very large numbers for ab-initio techniques with explicit treatment of electron correlation. Thus, the size of the molecules that we can treat with conventional methods is limited. Linear scaling methods have been developed for ab-initio, DFT and semi-empirical methods, but only the latter are currently able to treat complete enzymes. There are two different approaches available. 

The conformation-dependent chirality code constitutes a more general description of molecular chirality, which is formally comparable with the CICC [43], The main difference is that chiral carbon atoms arc now not explicitly considered, and combinations of any four atoms are now used, independently of the existence or nonexistence of chiial centers, and of their belonging or not belonging to ligands of chiral centers. 

A back end program essentially acts as a computational server for the front end. It receivcsinpiit, computes something, sendsit back to the front end and then looks for further input or commands from the front end. It can be used over and over for different cal-cii lation s. If it has been explicitly stopped, the Iron t end will start... 

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