Periodic Trajectories

It is sometimes very usefiil to look at a trajectory such as the synnnetric or antisynnnetric stretch of figure Al.2.5 and figure A1.2.6 not in the physical spatial coordinates (r. . r y), but in the phase space of Hamiltonian mechanics [16, 29], which in addition to the coordinates (r. . r ) also has as additional coordinates the set of conjugate momenta. . pj. ). In phase space, a one-diniensional trajectory such as the aiitisymmetric stretch again appears as a one-diniensional curve, but now the curve closes on itself Such a trajectory is referred to in nonlinear dynamics as a periodic orbit [29]. One says that the aihiamionic nonnal modes of Moser and Weinstein are stable periodic orbits. 

The classical counterpart of resonances is periodic orbits [91, 95, 96, 97 and 98]. For example, a purely classical study of the H+H2 collinear potential surface reveals that near the transition state for the H+H2 H2+H reaction there are several trajectories (in R and r) that are periodic. These trajectories are not stable but they nevertheless affect strongly tire quantum dynamics. A study of tlie resonances in H+H2 scattering as well as many other triatomic systems (see, e.g., [99]) reveals that the scattering peaks are closely related to tlie frequencies of the periodic orbits and the resonance wavefiinctions are large in the regions of space where the periodic orbits reside. 

Figure Cl.5.8. Spectral jumping of a single molecule of terrylene in polyethylene at 1.5 K. The upper trace displays fluorescence excitation spectra of tire same single molecule taken over two different 20 s time intervals, showing tire same molecule absorbing at two distinctly different frequencies. The lower panel plots tire peak frequency in tire fluorescence excitation spectmm as a function of time over a 40 min trajectory. The molecule undergoes discrete jumps among four (briefly five) different resonant frequencies during tliis time period. Arrows represent scans during which tire molecule had jumped entirely outside tire 10 GHz scan window. Adapted from...

C3.6.1(a )), from right to left. Suppose that at time the trajectory intersects this Poincare surface at a point (c (tg), C3 (Sq)), at time it makes its next or so-called first reium to the surface at point (c (tj), c 3 (t )). This process continues for times t, .. the difference being the period of the th first-return trajectory segment. The... 

Figure C3.6.6 The figure shows tire coordinate, for < 0, of tire family of trajectories intersecting tire Poincare surface at cq = 8.5 as a function of bifurcation parameter k 2- As tire ordinate k 2 decreases, tire first subhannonic cascade is visible between k 2 0.1, tire value of tire first subhannonic bifurcation to k 2 0.083, tire subhannonic limit of tire first cascade. Periodic orbits tliat arise by tire tangent bifurcation mechanism associated witli type-I intennittency (see tire text for references) can also be seen for values of k 2 smaller tlian tliis subhannonic limit. The left side of tire figure ends at k 2 = 0.072, tire value corresponding to tire chaotic attractor shown in figure C3.6.1(a). Otlier regions of chaos can also be seen.

The cores of the spiral waves need not be stationary and can move in periodic, quasi-periodic or even chaotic flower trajectories [42, 43]. In addition, spatio-temporal chaos can arise if such spiral waves break up and the spiral wave fragments spawn pairs of new spirals [42, 44]. 

Accuracy, however, in biomolecular trajectories, must be defined somewhat subjectively. In the absence of exact reference data (from experiment or from an analytical solution), the convention has been to measure accuracy with respect to reference trajectories by a Verlet-like integrator [18, 19] at a timestep of 1 or 0.5 fs (about one tenth or one twentieth the period, respectively, of the fastest period an 0-H or N-H stretch). As pointed out by Deufihard et al. [20], these values are still larger than those needed to... 

Fig. 5. Langevin trajectories for a harmonic oscillator of angular frequency u = 1 and unit mass simulated by a Verlet-like method (extended to Langevin dynamics) at a timestep of 0.1 (about 1/60 the period) for various 7. Shown for each 7 are plots for position versus time and phase-space diagrams.

The model consists of a two dimensional harmonic oscillator with mass 1 and force constants of 1 and 25. In Fig. 1 we show trajectories of the two oscillators computed with two time steps. When the time step is sufficiently small compared to the period of the fast oscillator an essentially exact result is obtained. If the time step is large then only the slow vibration persists, and is quite accurate. The filtering effect is consistent (of course) with our analytical analysis. Similar effects were demonstrated for more complex systems [7]. 

Computational issues that are pertinent in MD simulations are time complexity of the force calculations and the accuracy of the particle trajectories including other necessary quantitative measures. These two issues overwhelm computational scientists in several ways. MD simulations are done for long time periods and since numerical integration techniques involve discretization errors and stability restrictions which when not put in check, may corrupt the numerical solutions in such a way that they do not have any meaning and therefore, no useful inferences can be drawn from them. Different strategies such as globally stable numerical integrators and multiple time steps implementations have been used in this respect (see [27, 31]). 

One drawback to a molecular dynamics simulation is that the trajectory length calculated in a reasonable time is several orders of magnitude shorter than any chemical process and most physical processes, which occur in nanoseconds or longer. This allows yon to study properties that change w ithin shorter time periods (such as energy finctnations and atomic positions), but not long-term processes like protein folding. 

In many molecular dynamics simulations, equilibration is a separate step that precedes data collection. Equilibration is generally necessary lo avoid introducing artifacts during the healing step an d to en su re th at the trajectory is aciii ally sim u laiin g eq u i librium properties. The period required for equilibration depends on the property of Interest and the molecular system. It may take about 100 ps for the system to approach equilibrium, but some properties are fairly stable after 1 0-20 ps. Suggested tim es range from. 5 ps to nearly 100 ps for medium-si/ed proteins. 

HyperChem run s the molecular dynain ics trajectory, averaging and analyzing a trajectory and creating the Cartesian coordinates and velocities, fhe period for reporting these coordinates and velocities is th e data collection period. At-2. It is a m iiltiplc of the basic time step. At = ii At], and is also referred to as a data step. The value 1I2 is set in the Molecular Dynamics options dialog box. 

HyperChem can store a file of snapshots of a trajectory for subsequent analysis, fhe period for doing so is referred lo as the Snap-... 

TlyperCi hem updates the screen diirin g a trajectory at regular in ter-vals so yon can visiiali/e the irajectory. Since this screen update may slow down a trajectory If it occurs too frequently, yon c.an specify the duration of the Screen Refresh period At.,. The screen updates at ilines tQ, Iq + Atj, to + 2Atj, etc. The Screen Refresh period is specified in the Molecular Dynamics options dialog box by n 5 data steps, i.e. as a m iiliiplc of the data collection period, At5 = n 5 At2-... 

HyperChem includes a number of time periods associated with a trajectory. These include the basic time step in the integration of Newton s equations plus various multiples of this associated with collecting data, the forming of statistical averages, etc. The fundamental time period is Atj s At, the integration time step stt in the Molecular Dynamics dialog box. 

To create a set of snapshots of any molecular dynamics run, press the Snapshot button of the Molecular Dynamics Options dialog box to bring up the Molecular Dynamics Snapshots dialog box for naming a snapshot file. A snapshot file contains snapshots of the coordinates and velocities of a molecular system along the trajectory. The dialog box allows you to name the file and decide at what frequency to take snapshots. For example, choosing the snapshot period to be two data steps implies that only every other time step is stored in the snapshot file. 

The Z-spray inlet causes ions and neutrals to follow different paths after they have been formed from the electrically charged spray produced from a narrow inlet tube. The ions can be drawn into a mass analyzer after most of the solvent has evaporated away. The inlet derives its name from the Z-shaped trajectory taken by the ions, which ensures that there is little buildup of products on the narrow skimmer entrance into the mass spectrometer analyzer region. Consequently, in contrast to a conventional electrospray source, the skimmer does not need to be cleaned frequently and the sensitivity and performance of the instrument remain constant for long periods of time. 

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