Initial velocity files

The data files are ascii text files arranged in columns separated by space, tabs, or commas with header lines. Equilibrium files contain total ligand concentrations in the first column and free ligand concentrations in the second column. Initial velocity files contain substrate concentrations in the first column and initial velocities of duplicate assays in the subsequent columns. Progress curve files contain time in the first column and the measured experimental signal in the second column. 

The Restart check box can be used in ctiii junction with the explicit editing of a IIIX file to assign completely user-specified initial velocities. This may be useful in classical trajectory analysis of chemical reactions where the initial velocities and directions of the reactants are varied to statistically determine the probability of reaction occurring, or n ot, in the process of calculating a rate con -Stan t. 

Coordin ates of atom s can he set by n orm al translation orrotation of HyperCh cm molecules, fo set initial velocities, however, it is necessary to edit th e H l. file explicitly. The tin it o f velocity in the HIN file is. An gstrom s/picosecon d.. Areact.hin file and a script react.scr are in eluded with HyperChem to illustrate one simple reacting trajectory. In order to have these initial velocities used in a trajectory the Restart check box of the Molecular Dynamics Option s dialog box must he checked. If it is n ot, the in itial velocities in the HIN file will be ignored and a re-equilibration to the tern peratiire f of th e Molecular Dyn am ics Option s dialog box will occur. This destroys any imposed initial conditions on the molecular dynamics trajectory. 

In the laboratory, the well-defined direction is that of the initial velocity v. Therefore the laboratory orientation angle yl is defined as the angle that the axis of the molecule makes with respect to v. For low impact parameters the two angles are essentially the same because R is essentially in the direction of v and the collision is nearly head on. Otherwise, a transformation is needed. Implicit in such a transformation and in our entire discussion is the assumption that the axis of the molecule is hardly rotating during the collision. Dynamicists are very used to file idea that rotation of molecules is slow compared with the duration of a collision or a vibrational motion. That is correct, and is why experiments using selected reactants can demonstrate the reactive asymmetry between the two ends of a molecule. On the other hand, the intermolecular forces are not isotropic and can channel reactants preferentially into the cone of reaction or away from it. Only the detailed computations that we discuss in Chapter 5 can fully address such issues. 

The baseline reactor conditions in the following reactor analysis are susceptor temperature Ts = 1273 K, inlet temperature Tm = 333 K, reactor pressure p = 400 mTorr, gas velocity through the inlet manifold Vin = 100 cm/s, and the gap between inlet and susceptor L = 1 cm. Incoming gas-mixture mole fractions (e.g., from a gas-cylinder) are TEOS 0.25 and N2 (carrier gas) 0.75. You may use the files teos. gas and teos. surf for the gas-phase and surface reaction mechanisms. (Hint You may need the following initial guesses at the surface species site fractions SiG3(OH) 0.98, SiGsE 0.02, SiG(OH)2E 0.001. More details on the surface reaction mechanism and nomenclature are found in Ref. [69].)... 

If the initial scans at the desired velocity show no signs of leakage, click to open the Method window. Specify the number of scans (usually no more than 60) and close the box. Open the Options window and check the No delay calibration option. If you want the rotor to stop automatically after data collection, check the Stop XL after last scan option. Save the file by clicking on Savefile as from the drop down list in the File section. 

Here the variables xldot, x2dot, x3dot, and x4dot correspond to the derivatives of the state variables, in this case positions and velocities for the two masses. The expressions for this variable represent the four first-order differential equations of the system. These are integrated and the solution calculated using the ODE45 function in MATLAB. The values of the initial conditions and physical parameters need to be entered into another. m file to initialize the simulation in MATLAB and to enter... 

The conservation of the direction of the vector L implies that there is a particular, privileged, plane, such that the collision is confined to this special plane. This plane is defined, before the colhsion, by the two vectors R and v where v is the initial relative velocity. By its definition, Eq. (4.2), as a vector product, L is normal to this plane. We now want to show why, as time moves on, the collision remains confined to this plane. At some finite time t, consider the plane defined by the two vectors R(i) and R(i + At). Take At to be so small that R(t + At) = R(t) + (dR/dt)At and hence L is normal to the plane defined by R(t) and R(t + At). Since file direction of L is constant in time, for any value of t, R(t) is confined to file same single plane defined by the initial conditions. 

Simulations were started from the a-fcc structure, with initial translational and rotational velocities randomly assigned from uniform distributions, and 2 x 10 time steps run to assure well-equilibrated systems. Then, standard production runs were performed to cover between about 30-150 ps of elapsed time during which we calculated thermodynamic and structural properties. Additional files were created during the simulations for later processing and for visualization purposes. The thermodynamic properties were evaluated by partitioning the run into 10 independent sub-runs from which the averages and estimated standard deviations were obtained. For the case of NPT runs, the initial densities and set point pressures were taken from their NVT counterparts. 

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